Diff for /imach/src/imach.c between versions 1.36 and 1.91

version 1.36, 2002/03/29 15:27:27 version 1.91, 2003/06/25 15:30:29
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.91  2003/06/25 15:30:29  brouard
      * imach.c (Repository): Duplicated warning errors corrected.
   This program computes Healthy Life Expectancies from    (Repository): Elapsed time after each iteration is now output. It
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    helps to forecast when convergence will be reached. Elapsed time
   first survey ("cross") where individuals from different ages are    is stamped in powell.  We created a new html file for the graphs
   interviewed on their health status or degree of disability (in the    concerning matrix of covariance. It has extension -cov.htm.
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.90  2003/06/24 12:34:15  brouard
   (if any) in individual health status.  Health expectancies are    (Module): Some bugs corrected for windows. Also, when
   computed from the time spent in each health state according to a    mle=-1 a template is output in file "or"mypar.txt with the design
   model. More health states you consider, more time is necessary to reach the    of the covariance matrix to be input.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.89  2003/06/24 12:30:52  brouard
   probabibility to be observed in state j at the second wave    (Module): Some bugs corrected for windows. Also, when
   conditional to be observed in state i at the first wave. Therefore    mle=-1 a template is output in file "or"mypar.txt with the design
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    of the covariance matrix to be input.
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.88  2003/06/23 17:54:56  brouard
   where the markup *Covariates have to be included here again* invites    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.86  2003/06/17 20:04:08  brouard
   identical for each individual. Also, if a individual missed an    (Module): Change position of html and gnuplot routines and added
   intermediate interview, the information is lost, but taken into    routine fileappend.
   account using an interpolation or extrapolation.    
     Revision 1.85  2003/06/17 13:12:43  brouard
   hPijx is the probability to be observed in state i at age x+h    * imach.c (Repository): Check when date of death was earlier that
   conditional to the observed state i at age x. The delay 'h' can be    current date of interview. It may happen when the death was just
   split into an exact number (nh*stepm) of unobserved intermediate    prior to the death. In this case, dh was negative and likelihood
   states. This elementary transition (by month or quarter trimester,    was wrong (infinity). We still send an "Error" but patch by
   semester or year) is model as a multinomial logistic.  The hPx    assuming that the date of death was just one stepm after the
   matrix is simply the matrix product of nh*stepm elementary matrices    interview.
   and the contribution of each individual to the likelihood is simply    (Repository): Because some people have very long ID (first column)
   hPijx.    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
   Also this programme outputs the covariance matrix of the parameters but also    truncation)
   of the life expectancies. It also computes the prevalence limits.    (Repository): No more line truncation errors.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.84  2003/06/13 21:44:43  brouard
            Institut national d'études démographiques, Paris.    * imach.c (Repository): Replace "freqsummary" at a correct
   This software have been partly granted by Euro-REVES, a concerted action    place. It differs from routine "prevalence" which may be called
   from the European Union.    many times. Probs is memory consuming and must be used with
   It is copyrighted identically to a GNU software product, ie programme and    parcimony.
   software can be distributed freely for non commercial use. Latest version    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.83  2003/06/10 13:39:11  lievre
      *** empty log message ***
 #include <math.h>  
 #include <stdio.h>    Revision 1.82  2003/06/05 15:57:20  brouard
 #include <stdlib.h>    Add log in  imach.c and  fullversion number is now printed.
 #include <unistd.h>  
   */
 #define MAXLINE 256  /*
 #define GNUPLOTPROGRAM "wgnuplot"     Interpolated Markov Chain
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Short summary of the programme:
 /*#define DEBUG*/    
 #define windows    This program computes Healthy Life Expectancies from
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    case of a health survey which is our main interest) -2- at least a
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 #define NINTERVMAX 8    computed from the time spent in each health state according to a
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    model. More health states you consider, more time is necessary to reach the
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Maximum Likelihood of the parameters involved in the model.  The
 #define NCOVMAX 8 /* Maximum number of covariates */    simplest model is the multinomial logistic model where pij is the
 #define MAXN 20000    probability to be observed in state j at the second wave
 #define YEARM 12. /* Number of months per year */    conditional to be observed in state i at the first wave. Therefore
 #define AGESUP 130    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define AGEBASE 40    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 int erreur; /* Error number */    you to do it.  More covariates you add, slower the
 int nvar;    convergence.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    The advantage of this computer programme, compared to a simple
 int nlstate=2; /* Number of live states */    multinomial logistic model, is clear when the delay between waves is not
 int ndeath=1; /* Number of dead states */    identical for each individual. Also, if a individual missed an
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    intermediate interview, the information is lost, but taken into
 int popbased=0;    account using an interpolation or extrapolation.  
   
 int *wav; /* Number of waves for this individuual 0 is possible */    hPijx is the probability to be observed in state i at age x+h
 int maxwav; /* Maxim number of waves */    conditional to the observed state i at age x. The delay 'h' can be
 int jmin, jmax; /* min, max spacing between 2 waves */    split into an exact number (nh*stepm) of unobserved intermediate
 int mle, weightopt;    states. This elementary transition (by month, quarter,
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    semester or year) is modelled as a multinomial logistic.  The hPx
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    matrix is simply the matrix product of nh*stepm elementary matrices
 double jmean; /* Mean space between 2 waves */    and the contribution of each individual to the likelihood is simply
 double **oldm, **newm, **savm; /* Working pointers to matrices */    hPijx.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Also this programme outputs the covariance matrix of the parameters but also
 FILE *ficgp,*ficresprob,*ficpop;    of the life expectancies. It also computes the stable prevalence. 
 FILE *ficreseij;    
   char filerese[FILENAMELENGTH];    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
  FILE  *ficresvij;             Institut national d'études démographiques, Paris.
   char fileresv[FILENAMELENGTH];    This software have been partly granted by Euro-REVES, a concerted action
  FILE  *ficresvpl;    from the European Union.
   char fileresvpl[FILENAMELENGTH];    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define NR_END 1    can be accessed at http://euroreves.ined.fr/imach .
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define NRANSI    
 #define ITMAX 200    **********************************************************************/
   /*
 #define TOL 2.0e-4    main
     read parameterfile
 #define CGOLD 0.3819660    read datafile
 #define ZEPS 1.0e-10    concatwav
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    freqsummary
     if (mle >= 1)
 #define GOLD 1.618034      mlikeli
 #define GLIMIT 100.0    print results files
 #define TINY 1.0e-20    if mle==1 
        computes hessian
 static double maxarg1,maxarg2;    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))        begin-prev-date,...
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    open gnuplot file
      open html file
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    stable prevalence
 #define rint(a) floor(a+0.5)     for age prevalim()
     h Pij x
 static double sqrarg;    variance of p varprob
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    forecasting if prevfcast==1 prevforecast call prevalence()
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    health expectancies
     Variance-covariance of DFLE
 int imx;    prevalence()
 int stepm;     movingaverage()
 /* Stepm, step in month: minimum step interpolation*/    varevsij() 
     if popbased==1 varevsij(,popbased)
 int estepm;    total life expectancies
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Variance of stable prevalence
    end
 int m,nb;  */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;   
   #include <math.h>
 double *weight;  #include <stdio.h>
 int **s; /* Status */  #include <stdlib.h>
 double *agedc, **covar, idx;  #include <unistd.h>
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   #include <sys/time.h>
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #include <time.h>
 double ftolhess; /* Tolerance for computing hessian */  #include "timeval.h"
   
 /**************** split *************************/  #define MAXLINE 256
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define GNUPLOTPROGRAM "gnuplot"
 {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
    char *s;                             /* pointer */  #define FILENAMELENGTH 132
    int  l1, l2;                         /* length counters */  /*#define DEBUG*/
   /*#define windows*/
    l1 = strlen( path );                 /* length of path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #else  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    s = strrchr( path, '/' );            /* find last / */  
 #endif  #define NINTERVMAX 8
    if ( s == NULL ) {                   /* no directory, so use current */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #if     defined(__bsd__)                /* get current working directory */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       extern char       *getwd( );  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
       if ( getwd( dirc ) == NULL ) {  #define YEARM 12. /* Number of months per year */
 #else  #define AGESUP 130
       extern char       *getcwd( );  #define AGEBASE 40
   #ifdef unix
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define DIRSEPARATOR '/'
 #endif  #define ODIRSEPARATOR '\\'
          return( GLOCK_ERROR_GETCWD );  #else
       }  #define DIRSEPARATOR '\\'
       strcpy( name, path );             /* we've got it */  #define ODIRSEPARATOR '/'
    } else {                             /* strip direcotry from path */  #endif
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  /* $Id$ */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  /* $State$ */
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
       dirc[l1-l2] = 0;                  /* add zero */  char fullversion[]="$Revision$ $Date$"; 
    }  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    l1 = strlen( dirc );                 /* length of directory */  int nvar;
 #ifdef windows  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int npar=NPARMAX;
 #else  int nlstate=2; /* Number of live states */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int ndeath=1; /* Number of dead states */
 #endif  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    s = strrchr( name, '.' );            /* find last / */  int popbased=0;
    s++;  
    strcpy(ext,s);                       /* save extension */  int *wav; /* Number of waves for this individuual 0 is possible */
    l1= strlen( name);  int maxwav; /* Maxim number of waves */
    l2= strlen( s)+1;  int jmin, jmax; /* min, max spacing between 2 waves */
    strncpy( finame, name, l1-l2);  int gipmx, gsw; /* Global variables on the number of contributions 
    finame[l1-l2]= 0;                     to the likelihood and the sum of weights (done by funcone)*/
    return( 0 );                         /* we're done */  int mle, weightopt;
 }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 /******************************************/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 void replace(char *s, char*t)  double **oldm, **newm, **savm; /* Working pointers to matrices */
 {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   int i;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   int lg=20;  FILE *ficlog, *ficrespow;
   i=0;  int globpr; /* Global variable for printing or not */
   lg=strlen(t);  double fretone; /* Only one call to likelihood */
   for(i=0; i<= lg; i++) {  long ipmx; /* Number of contributions */
     (s[i] = t[i]);  double sw; /* Sum of weights */
     if (t[i]== '\\') s[i]='/';  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   }  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 int nbocc(char *s, char occ)  FILE *fichtm, *fichtmcov; /* Html File */
 {  FILE *ficreseij;
   int i,j=0;  char filerese[FILENAMELENGTH];
   int lg=20;  FILE  *ficresvij;
   i=0;  char fileresv[FILENAMELENGTH];
   lg=strlen(s);  FILE  *ficresvpl;
   for(i=0; i<= lg; i++) {  char fileresvpl[FILENAMELENGTH];
   if  (s[i] == occ ) j++;  char title[MAXLINE];
   }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   return j;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 }  char tmpout[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
 void cutv(char *u,char *v, char*t, char occ)  int  outcmd=0;
 {  
   int i,lg,j,p=0;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   i=0;  char lfileres[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  char filelog[FILENAMELENGTH]; /* Log file */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char filerest[FILENAMELENGTH];
   }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
   lg=strlen(t);  
   for(j=0; j<p; j++) {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     (u[j] = t[j]);  
   }  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
      u[p]='\0';  struct timezone tzp;
   extern int gettimeofday();
    for(j=0; j<= lg; j++) {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     if (j>=(p+1))(v[j-p-1] = t[j]);  long time_value;
   }  extern long time();
 }  char strcurr[80], strfor[80];
   
 /********************** nrerror ********************/  #define NR_END 1
   #define FREE_ARG char*
 void nrerror(char error_text[])  #define FTOL 1.0e-10
 {  
   fprintf(stderr,"ERREUR ...\n");  #define NRANSI 
   fprintf(stderr,"%s\n",error_text);  #define ITMAX 200 
   exit(1);  
 }  #define TOL 2.0e-4 
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  #define CGOLD 0.3819660 
 {  #define ZEPS 1.0e-10 
   double *v;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #define GOLD 1.618034 
   return v-nl+NR_END;  #define GLIMIT 100.0 
 }  #define TINY 1.0e-20 
   
 /************************ free vector ******************/  static double maxarg1,maxarg2;
 void free_vector(double*v, int nl, int nh)  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   free((FREE_ARG)(v+nl-NR_END));    
 }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   int *v;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  int imx; 
   return v-nl+NR_END;  int stepm;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /******************free ivector **************************/  int estepm;
 void free_ivector(int *v, long nl, long nh)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   free((FREE_ARG)(v+nl-NR_END));  int m,nb;
 }  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 /******************* imatrix *******************************/  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  double **pmmij, ***probs;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  double dateintmean=0;
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  double *weight;
   int **m;  int **s; /* Status */
    double *agedc, **covar, idx;
   /* allocate pointers to rows */  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   m += NR_END;  double ftolhess; /* Tolerance for computing hessian */
   m -= nrl;  
    /**************** split *************************/
    static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   /* allocate rows and set pointers to them */  {
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    char  *ss;                            /* pointer */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int   l1, l2;                         /* length counters */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    l1 = strlen(path );                   /* length of path */
      if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so use current */
   /* return pointer to array of pointers to rows */      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   return m;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 /****************** free_imatrix *************************/      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 void free_imatrix(m,nrl,nrh,ncl,nch)        return( GLOCK_ERROR_GETCWD );
       int **m;      }
       long nch,ncl,nrh,nrl;      strcpy( name, path );               /* we've got it */
      /* free an int matrix allocated by imatrix() */    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      l2 = strlen( ss );                  /* length of filename */
   free((FREE_ARG) (m+nrl-NR_END));      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 }      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 /******************* matrix *******************************/      dirc[l1-l2] = 0;                    /* add zero */
 double **matrix(long nrl, long nrh, long ncl, long nch)    }
 {    l1 = strlen( dirc );                  /* length of directory */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    /*#ifdef windows
   double **m;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   #else
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   if (!m) nrerror("allocation failure 1 in matrix()");  #endif
   m += NR_END;    */
   m -= nrl;    ss = strrchr( name, '.' );            /* find last / */
     ss++;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    strcpy(ext,ss);                       /* save extension */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    l1= strlen( name);
   m[nrl] += NR_END;    l2= strlen(ss)+1;
   m[nrl] -= ncl;    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    return( 0 );                          /* we're done */
   return m;  }
 }  
   
 /*************************free matrix ************************/  /******************************************/
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  void replace_back_to_slash(char *s, char*t)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  {
   free((FREE_ARG)(m+nrl-NR_END));    int i;
 }    int lg=0;
     i=0;
 /******************* ma3x *******************************/    lg=strlen(t);
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    for(i=0; i<= lg; i++) {
 {      (s[i] = t[i]);
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;      if (t[i]== '\\') s[i]='/';
   double ***m;    }
   }
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  int nbocc(char *s, char occ)
   m += NR_END;  {
   m -= nrl;    int i,j=0;
     int lg=20;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    i=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    lg=strlen(s);
   m[nrl] += NR_END;    for(i=0; i<= lg; i++) {
   m[nrl] -= ncl;    if  (s[i] == occ ) j++;
     }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    return j;
   }
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  void cutv(char *u,char *v, char*t, char occ)
   m[nrl][ncl] += NR_END;  {
   m[nrl][ncl] -= nll;    /* cuts string t into u and v where u is ended by char occ excluding it
   for (j=ncl+1; j<=nch; j++)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
     m[nrl][j]=m[nrl][j-1]+nlay;       gives u="abcedf" and v="ghi2j" */
      int i,lg,j,p=0;
   for (i=nrl+1; i<=nrh; i++) {    i=0;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    for(j=0; j<=strlen(t)-1; j++) {
     for (j=ncl+1; j<=nch; j++)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       m[i][j]=m[i][j-1]+nlay;    }
   }  
   return m;    lg=strlen(t);
 }    for(j=0; j<p; j++) {
       (u[j] = t[j]);
 /*************************free ma3x ************************/    }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)       u[p]='\0';
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));     for(j=0; j<= lg; j++) {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      if (j>=(p+1))(v[j-p-1] = t[j]);
   free((FREE_ARG)(m+nrl-NR_END));    }
 }  }
   
 /***************** f1dim *************************/  /********************** nrerror ********************/
 extern int ncom;  
 extern double *pcom,*xicom;  void nrerror(char error_text[])
 extern double (*nrfunc)(double []);  {
      fprintf(stderr,"ERREUR ...\n");
 double f1dim(double x)    fprintf(stderr,"%s\n",error_text);
 {    exit(EXIT_FAILURE);
   int j;  }
   double f;  /*********************** vector *******************/
   double *xt;  double *vector(int nl, int nh)
    {
   xt=vector(1,ncom);    double *v;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   f=(*nrfunc)(xt);    if (!v) nrerror("allocation failure in vector");
   free_vector(xt,1,ncom);    return v-nl+NR_END;
   return f;  }
 }  
   /************************ free vector ******************/
 /*****************brent *************************/  void free_vector(double*v, int nl, int nh)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  {
 {    free((FREE_ARG)(v+nl-NR_END));
   int iter;  }
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /************************ivector *******************************/
   double ftemp;  int *ivector(long nl,long nh)
   double p,q,r,tol1,tol2,u,v,w,x,xm;  {
   double e=0.0;    int *v;
      v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   a=(ax < cx ? ax : cx);    if (!v) nrerror("allocation failure in ivector");
   b=(ax > cx ? ax : cx);    return v-nl+NR_END;
   x=w=v=bx;  }
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  /******************free ivector **************************/
     xm=0.5*(a+b);  void free_ivector(int *v, long nl, long nh)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  {
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    free((FREE_ARG)(v+nl-NR_END));
     printf(".");fflush(stdout);  }
 #ifdef DEBUG  
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  /************************lvector *******************************/
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  long *lvector(long nl,long nh)
 #endif  {
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    long *v;
       *xmin=x;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       return fx;    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
     ftemp=fu;  }
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  /******************free lvector **************************/
       q=(x-v)*(fx-fw);  void free_lvector(long *v, long nl, long nh)
       p=(x-v)*q-(x-w)*r;  {
       q=2.0*(q-r);    free((FREE_ARG)(v+nl-NR_END));
       if (q > 0.0) p = -p;  }
       q=fabs(q);  
       etemp=e;  /******************* imatrix *******************************/
       e=d;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  { 
       else {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         d=p/q;    int **m; 
         u=x+d;    
         if (u-a < tol2 || b-u < tol2)    /* allocate pointers to rows */ 
           d=SIGN(tol1,xm-x);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     } else {    m += NR_END; 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    m -= nrl; 
     }    
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    
     fu=(*f)(u);    /* allocate rows and set pointers to them */ 
     if (fu <= fx) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       if (u >= x) a=x; else b=x;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       SHFT(v,w,x,u)    m[nrl] += NR_END; 
         SHFT(fv,fw,fx,fu)    m[nrl] -= ncl; 
         } else {    
           if (u < x) a=u; else b=u;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
           if (fu <= fw || w == x) {    
             v=w;    /* return pointer to array of pointers to rows */ 
             w=u;    return m; 
             fv=fw;  } 
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  /****************** free_imatrix *************************/
             v=u;  void free_imatrix(m,nrl,nrh,ncl,nch)
             fv=fu;        int **m;
           }        long nch,ncl,nrh,nrl; 
         }       /* free an int matrix allocated by imatrix() */ 
   }  { 
   nrerror("Too many iterations in brent");    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   *xmin=x;    free((FREE_ARG) (m+nrl-NR_END)); 
   return fx;  } 
 }  
   /******************* matrix *******************************/
 /****************** mnbrak ***********************/  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
             double (*func)(double))    double **m;
 {  
   double ulim,u,r,q, dum;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double fu;    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
   *fa=(*func)(*ax);    m -= nrl;
   *fb=(*func)(*bx);  
   if (*fb > *fa) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     SHFT(dum,*ax,*bx,dum)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       SHFT(dum,*fb,*fa,dum)    m[nrl] += NR_END;
       }    m[nrl] -= ncl;
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   while (*fb > *fc) {    return m;
     r=(*bx-*ax)*(*fb-*fc);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     q=(*bx-*cx)*(*fb-*fa);     */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  }
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  /*************************free matrix ************************/
     if ((*bx-u)*(u-*cx) > 0.0) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       fu=(*func)(u);  {
     } else if ((*cx-u)*(u-ulim) > 0.0) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       fu=(*func)(u);    free((FREE_ARG)(m+nrl-NR_END));
       if (fu < *fc) {  }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  /******************* ma3x *******************************/
           }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  {
       u=ulim;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       fu=(*func)(u);    double ***m;
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       fu=(*func)(u);    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     SHFT(*ax,*bx,*cx,u)    m -= nrl;
       SHFT(*fa,*fb,*fc,fu)  
       }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 /*************** linmin ************************/    m[nrl] -= ncl;
   
 int ncom;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 double *pcom,*xicom;  
 double (*nrfunc)(double []);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
      if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    m[nrl][ncl] += NR_END;
 {    m[nrl][ncl] -= nll;
   double brent(double ax, double bx, double cx,    for (j=ncl+1; j<=nch; j++) 
                double (*f)(double), double tol, double *xmin);      m[nrl][j]=m[nrl][j-1]+nlay;
   double f1dim(double x);    
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    for (i=nrl+1; i<=nrh; i++) {
               double *fc, double (*func)(double));      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   int j;      for (j=ncl+1; j<=nch; j++) 
   double xx,xmin,bx,ax;        m[i][j]=m[i][j-1]+nlay;
   double fx,fb,fa;    }
      return m; 
   ncom=n;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   pcom=vector(1,n);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   xicom=vector(1,n);    */
   nrfunc=func;  }
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  /*************************free ma3x ************************/
     xicom[j]=xi[j];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   }  {
   ax=0.0;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   xx=1.0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    free((FREE_ARG)(m+nrl-NR_END));
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  }
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /***************** f1dim *************************/
 #endif  extern int ncom; 
   for (j=1;j<=n;j++) {  extern double *pcom,*xicom;
     xi[j] *= xmin;  extern double (*nrfunc)(double []); 
     p[j] += xi[j];   
   }  double f1dim(double x) 
   free_vector(xicom,1,n);  { 
   free_vector(pcom,1,n);    int j; 
 }    double f;
     double *xt; 
 /*************** powell ************************/   
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    xt=vector(1,ncom); 
             double (*func)(double []))    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 {    f=(*nrfunc)(xt); 
   void linmin(double p[], double xi[], int n, double *fret,    free_vector(xt,1,ncom); 
               double (*func)(double []));    return f; 
   int i,ibig,j;  } 
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  /*****************brent *************************/
   double *xits;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   pt=vector(1,n);  { 
   ptt=vector(1,n);    int iter; 
   xit=vector(1,n);    double a,b,d,etemp;
   xits=vector(1,n);    double fu,fv,fw,fx;
   *fret=(*func)(p);    double ftemp;
   for (j=1;j<=n;j++) pt[j]=p[j];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   for (*iter=1;;++(*iter)) {    double e=0.0; 
     fp=(*fret);   
     ibig=0;    a=(ax < cx ? ax : cx); 
     del=0.0;    b=(ax > cx ? ax : cx); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    x=w=v=bx; 
     for (i=1;i<=n;i++)    fw=fv=fx=(*f)(x); 
       printf(" %d %.12f",i, p[i]);    for (iter=1;iter<=ITMAX;iter++) { 
     printf("\n");      xm=0.5*(a+b); 
     for (i=1;i<=n;i++) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       fptt=(*fret);      printf(".");fflush(stdout);
 #ifdef DEBUG      fprintf(ficlog,".");fflush(ficlog);
       printf("fret=%lf \n",*fret);  #ifdef DEBUG
 #endif      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       printf("%d",i);fflush(stdout);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       linmin(p,xit,n,fret,func);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       if (fabs(fptt-(*fret)) > del) {  #endif
         del=fabs(fptt-(*fret));      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         ibig=i;        *xmin=x; 
       }        return fx; 
 #ifdef DEBUG      } 
       printf("%d %.12e",i,(*fret));      ftemp=fu;
       for (j=1;j<=n;j++) {      if (fabs(e) > tol1) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        r=(x-w)*(fx-fv); 
         printf(" x(%d)=%.12e",j,xit[j]);        q=(x-v)*(fx-fw); 
       }        p=(x-v)*q-(x-w)*r; 
       for(j=1;j<=n;j++)        q=2.0*(q-r); 
         printf(" p=%.12e",p[j]);        if (q > 0.0) p = -p; 
       printf("\n");        q=fabs(q); 
 #endif        etemp=e; 
     }        e=d; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 #ifdef DEBUG          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       int k[2],l;        else { 
       k[0]=1;          d=p/q; 
       k[1]=-1;          u=x+d; 
       printf("Max: %.12e",(*func)(p));          if (u-a < tol2 || b-u < tol2) 
       for (j=1;j<=n;j++)            d=SIGN(tol1,xm-x); 
         printf(" %.12e",p[j]);        } 
       printf("\n");      } else { 
       for(l=0;l<=1;l++) {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         for (j=1;j<=n;j++) {      } 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      fu=(*f)(u); 
         }      if (fu <= fx) { 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        if (u >= x) a=x; else b=x; 
       }        SHFT(v,w,x,u) 
 #endif          SHFT(fv,fw,fx,fu) 
           } else { 
             if (u < x) a=u; else b=u; 
       free_vector(xit,1,n);            if (fu <= fw || w == x) { 
       free_vector(xits,1,n);              v=w; 
       free_vector(ptt,1,n);              w=u; 
       free_vector(pt,1,n);              fv=fw; 
       return;              fw=fu; 
     }            } else if (fu <= fv || v == x || v == w) { 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");              v=u; 
     for (j=1;j<=n;j++) {              fv=fu; 
       ptt[j]=2.0*p[j]-pt[j];            } 
       xit[j]=p[j]-pt[j];          } 
       pt[j]=p[j];    } 
     }    nrerror("Too many iterations in brent"); 
     fptt=(*func)(ptt);    *xmin=x; 
     if (fptt < fp) {    return fx; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  } 
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /****************** mnbrak ***********************/
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           xi[j][n]=xit[j];              double (*func)(double)) 
         }  { 
 #ifdef DEBUG    double ulim,u,r,q, dum;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    double fu; 
         for(j=1;j<=n;j++)   
           printf(" %.12e",xit[j]);    *fa=(*func)(*ax); 
         printf("\n");    *fb=(*func)(*bx); 
 #endif    if (*fb > *fa) { 
       }      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
   }        } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 /**** Prevalence limit ****************/    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      q=(*bx-*cx)*(*fb-*fa); 
 {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
      matrix by transitions matrix until convergence is reached */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
   int i, ii,j,k;        fu=(*func)(u); 
   double min, max, maxmin, maxmax,sumnew=0.;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double **matprod2();        fu=(*func)(u); 
   double **out, cov[NCOVMAX], **pmij();        if (fu < *fc) { 
   double **newm;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double agefin, delaymax=50 ; /* Max number of years to converge */            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
   for (ii=1;ii<=nlstate+ndeath;ii++)      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     for (j=1;j<=nlstate+ndeath;j++){        u=ulim; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fu=(*func)(u); 
     }      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
    cov[1]=1.;        fu=(*func)(u); 
        } 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      SHFT(*ax,*bx,*cx,u) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        SHFT(*fa,*fb,*fc,fu) 
     newm=savm;        } 
     /* Covariates have to be included here again */  } 
      cov[2]=agefin;  
    /*************** linmin ************************/
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int ncom; 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  double *pcom,*xicom;
       }  double (*nrfunc)(double []); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];   
       for (k=1; k<=cptcovprod;k++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  { 
     double brent(double ax, double bx, double cx, 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/                 double (*f)(double), double tol, double *xmin); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    double f1dim(double x); 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);                double *fc, double (*func)(double)); 
     int j; 
     savm=oldm;    double xx,xmin,bx,ax; 
     oldm=newm;    double fx,fb,fa;
     maxmax=0.;   
     for(j=1;j<=nlstate;j++){    ncom=n; 
       min=1.;    pcom=vector(1,n); 
       max=0.;    xicom=vector(1,n); 
       for(i=1; i<=nlstate; i++) {    nrfunc=func; 
         sumnew=0;    for (j=1;j<=n;j++) { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      pcom[j]=p[j]; 
         prlim[i][j]= newm[i][j]/(1-sumnew);      xicom[j]=xi[j]; 
         max=FMAX(max,prlim[i][j]);    } 
         min=FMIN(min,prlim[i][j]);    ax=0.0; 
       }    xx=1.0; 
       maxmin=max-min;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       maxmax=FMAX(maxmax,maxmin);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
     if(maxmax < ftolpl){    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       return prlim;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
   }    for (j=1;j<=n;j++) { 
 }      xi[j] *= xmin; 
       p[j] += xi[j]; 
 /*************** transition probabilities ***************/    } 
     free_vector(xicom,1,n); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    free_vector(pcom,1,n); 
 {  } 
   double s1, s2;  
   /*double t34;*/  char *asc_diff_time(long time_sec, char ascdiff[])
   int i,j,j1, nc, ii, jj;  {
     long sec_left, days, hours, minutes;
     for(i=1; i<= nlstate; i++){    days = (time_sec) / (60*60*24);
     for(j=1; j<i;j++){    sec_left = (time_sec) % (60*60*24);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    hours = (sec_left) / (60*60) ;
         /*s2 += param[i][j][nc]*cov[nc];*/    sec_left = (sec_left) %(60*60);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    minutes = (sec_left) /60;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    sec_left = (sec_left) % (60);
       }    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       ps[i][j]=s2;    return ascdiff;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  }
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  /*************** powell ************************/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];              double (*func)(double [])) 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  { 
       }    void linmin(double p[], double xi[], int n, double *fret, 
       ps[i][j]=s2;                double (*func)(double [])); 
     }    int i,ibig,j; 
   }    double del,t,*pt,*ptt,*xit;
     /*ps[3][2]=1;*/    double fp,fptt;
     double *xits;
   for(i=1; i<= nlstate; i++){    int niterf, itmp;
      s1=0;  
     for(j=1; j<i; j++)    pt=vector(1,n); 
       s1+=exp(ps[i][j]);    ptt=vector(1,n); 
     for(j=i+1; j<=nlstate+ndeath; j++)    xit=vector(1,n); 
       s1+=exp(ps[i][j]);    xits=vector(1,n); 
     ps[i][i]=1./(s1+1.);    *fret=(*func)(p); 
     for(j=1; j<i; j++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    for (*iter=1;;++(*iter)) { 
     for(j=i+1; j<=nlstate+ndeath; j++)      fp=(*fret); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      ibig=0; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      del=0.0; 
   } /* end i */      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     for(jj=1; jj<= nlstate+ndeath; jj++){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       ps[ii][jj]=0;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       ps[ii][ii]=1;      for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
   }        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
       }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      printf("\n");
     for(jj=1; jj<= nlstate+ndeath; jj++){      fprintf(ficlog,"\n");
      printf("%lf ",ps[ii][jj]);      fprintf(ficrespow,"\n");fflush(ficrespow);
    }      if(*iter <=3){
     printf("\n ");        tm = *localtime(&curr_time.tv_sec);
     }        asctime_r(&tm,strcurr);
     printf("\n ");printf("%lf ",cov[2]);*/        forecast_time=curr_time;
 /*        itmp = strlen(strcurr);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        if(strcurr[itmp-1]=='\n')
   goto end;*/          strcurr[itmp-1]='\0';
     return ps;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
 /**************** Product of 2 matrices ******************/          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          asctime_r(&tmf,strfor);
 {  /*      strcpy(strfor,asctime(&tmf)); */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          itmp = strlen(strfor);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          if(strfor[itmp-1]=='\n')
   /* in, b, out are matrice of pointers which should have been initialized          strfor[itmp-1]='\0';
      before: only the contents of out is modified. The function returns          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
      a pointer to pointers identical to out */          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   long i, j, k;        }
   for(i=nrl; i<= nrh; i++)      }
     for(k=ncolol; k<=ncoloh; k++)      for (i=1;i<=n;i++) { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         out[i][k] +=in[i][j]*b[j][k];        fptt=(*fret); 
   #ifdef DEBUG
   return out;        printf("fret=%lf \n",*fret);
 }        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
         printf("%d",i);fflush(stdout);
 /************* Higher Matrix Product ***************/        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        if (fabs(fptt-(*fret)) > del) { 
 {          del=fabs(fptt-(*fret)); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          ibig=i; 
      duration (i.e. until        } 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  #ifdef DEBUG
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        printf("%d %.12e",i,(*fret));
      (typically every 2 years instead of every month which is too big).        fprintf(ficlog,"%d %.12e",i,(*fret));
      Model is determined by parameters x and covariates have to be        for (j=1;j<=n;j++) {
      included manually here.          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
      */          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   int i, j, d, h, k;        for(j=1;j<=n;j++) {
   double **out, cov[NCOVMAX];          printf(" p=%.12e",p[j]);
   double **newm;          fprintf(ficlog," p=%.12e",p[j]);
         }
   /* Hstepm could be zero and should return the unit matrix */        printf("\n");
   for (i=1;i<=nlstate+ndeath;i++)        fprintf(ficlog,"\n");
     for (j=1;j<=nlstate+ndeath;j++){  #endif
       oldm[i][j]=(i==j ? 1.0 : 0.0);      } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        int k[2],l;
   for(h=1; h <=nhstepm; h++){        k[0]=1;
     for(d=1; d <=hstepm; d++){        k[1]=-1;
       newm=savm;        printf("Max: %.12e",(*func)(p));
       /* Covariates have to be included here again */        fprintf(ficlog,"Max: %.12e",(*func)(p));
       cov[1]=1.;        for (j=1;j<=n;j++) {
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          printf(" %.12e",p[j]);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          fprintf(ficlog," %.12e",p[j]);
       for (k=1; k<=cptcovage;k++)        }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        printf("\n");
       for (k=1; k<=cptcovprod;k++)        fprintf(ficlog,"\n");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       savm=oldm;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       oldm=newm;        }
     }  #endif
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];        free_vector(xit,1,n); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        free_vector(xits,1,n); 
          */        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
   } /* end h */        return; 
   return po;      } 
 }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 /*************** log-likelihood *************/        xit[j]=p[j]-pt[j]; 
 double func( double *x)        pt[j]=p[j]; 
 {      } 
   int i, ii, j, k, mi, d, kk;      fptt=(*func)(ptt); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      if (fptt < fp) { 
   double **out;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   double sw; /* Sum of weights */        if (t < 0.0) { 
   double lli; /* Individual log likelihood */          linmin(p,xit,n,fret,func); 
   long ipmx;          for (j=1;j<=n;j++) { 
   /*extern weight */            xi[j][ibig]=xi[j][n]; 
   /* We are differentiating ll according to initial status */            xi[j][n]=xit[j]; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          }
   /*for(i=1;i<imx;i++)  #ifdef DEBUG
     printf(" %d\n",s[4][i]);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   cov[1]=1.;          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
   for(k=1; k<=nlstate; k++) ll[k]=0.;            fprintf(ficlog," %.12e",xit[j]);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          }
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          printf("\n");
     for(mi=1; mi<= wav[i]-1; mi++){          fprintf(ficlog,"\n");
       for (ii=1;ii<=nlstate+ndeath;ii++)  #endif
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        }
       for(d=0; d<dh[mi][i]; d++){      } 
         newm=savm;    } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  } 
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  /**** Prevalence limit (stable prevalence)  ****************/
         }  
          double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  {
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         savm=oldm;       matrix by transitions matrix until convergence is reached */
         oldm=newm;  
            int i, ii,j,k;
            double min, max, maxmin, maxmax,sumnew=0.;
       } /* end mult */    double **matprod2();
          double **out, cov[NCOVMAX], **pmij();
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double **newm;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double agefin, delaymax=50 ; /* Max number of years to converge */
       ipmx +=1;  
       sw += weight[i];    for (ii=1;ii<=nlstate+ndeath;ii++)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      for (j=1;j<=nlstate+ndeath;j++){
     } /* end of wave */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   } /* end of individual */      }
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];     cov[1]=1.;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */   
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   return -l;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 }      newm=savm;
       /* Covariates have to be included here again */
        cov[2]=agefin;
 /*********** Maximum Likelihood Estimation ***************/    
         for (k=1; k<=cptcovn;k++) {
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 {          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   int i,j, iter;        }
   double **xi,*delti;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double fret;        for (k=1; k<=cptcovprod;k++)
   xi=matrix(1,npar,1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       xi[i][j]=(i==j ? 1.0 : 0.0);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   printf("Powell\n");        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   powell(p,xi,npar,ftol,&iter,&fret,func);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      savm=oldm;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      oldm=newm;
       maxmax=0.;
 }      for(j=1;j<=nlstate;j++){
         min=1.;
 /**** Computes Hessian and covariance matrix ***/        max=0.;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        for(i=1; i<=nlstate; i++) {
 {          sumnew=0;
   double  **a,**y,*x,pd;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   double **hess;          prlim[i][j]= newm[i][j]/(1-sumnew);
   int i, j,jk;          max=FMAX(max,prlim[i][j]);
   int *indx;          min=FMIN(min,prlim[i][j]);
         }
   double hessii(double p[], double delta, int theta, double delti[]);        maxmin=max-min;
   double hessij(double p[], double delti[], int i, int j);        maxmax=FMAX(maxmax,maxmin);
   void lubksb(double **a, int npar, int *indx, double b[]) ;      }
   void ludcmp(double **a, int npar, int *indx, double *d) ;      if(maxmax < ftolpl){
         return prlim;
   hess=matrix(1,npar,1,npar);      }
     }
   printf("\nCalculation of the hessian matrix. Wait...\n");  }
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);  /*************** transition probabilities ***************/ 
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     /*printf(" %lf ",hess[i][i]);*/  {
   }    double s1, s2;
      /*double t34;*/
   for (i=1;i<=npar;i++) {    int i,j,j1, nc, ii, jj;
     for (j=1;j<=npar;j++)  {  
       if (j>i) {      for(i=1; i<= nlstate; i++){
         printf(".%d%d",i,j);fflush(stdout);      for(j=1; j<i;j++){
         hess[i][j]=hessij(p,delti,i,j);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         hess[j][i]=hess[i][j];              /*s2 += param[i][j][nc]*cov[nc];*/
         /*printf(" %lf ",hess[i][j]);*/          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       }          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
     }        }
   }        ps[i][j]=s2;
   printf("\n");        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      for(j=i+1; j<=nlstate+ndeath;j++){
          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   a=matrix(1,npar,1,npar);          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   y=matrix(1,npar,1,npar);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   x=vector(1,npar);        }
   indx=ivector(1,npar);        ps[i][j]=s2;
   for (i=1;i<=npar;i++)      }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    }
   ludcmp(a,npar,indx,&pd);      /*ps[3][2]=1;*/
   
   for (j=1;j<=npar;j++) {    for(i=1; i<= nlstate; i++){
     for (i=1;i<=npar;i++) x[i]=0;       s1=0;
     x[j]=1;      for(j=1; j<i; j++)
     lubksb(a,npar,indx,x);        s1+=exp(ps[i][j]);
     for (i=1;i<=npar;i++){      for(j=i+1; j<=nlstate+ndeath; j++)
       matcov[i][j]=x[i];        s1+=exp(ps[i][j]);
     }      ps[i][i]=1./(s1+1.);
   }      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
   printf("\n#Hessian matrix#\n");      for(j=i+1; j<=nlstate+ndeath; j++)
   for (i=1;i<=npar;i++) {        ps[i][j]= exp(ps[i][j])*ps[i][i];
     for (j=1;j<=npar;j++) {      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       printf("%.3e ",hess[i][j]);    } /* end i */
     }  
     printf("\n");    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   }      for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][jj]=0;
   /* Recompute Inverse */        ps[ii][ii]=1;
   for (i=1;i<=npar;i++)      }
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    }
   ludcmp(a,npar,indx,&pd);  
   
   /*  printf("\n#Hessian matrix recomputed#\n");    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   for (j=1;j<=npar;j++) {       printf("%lf ",ps[ii][jj]);
     for (i=1;i<=npar;i++) x[i]=0;     }
     x[j]=1;      printf("\n ");
     lubksb(a,npar,indx,x);      }
     for (i=1;i<=npar;i++){      printf("\n ");printf("%lf ",cov[2]);*/
       y[i][j]=x[i];  /*
       printf("%.3e ",y[i][j]);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     }    goto end;*/
     printf("\n");      return ps;
   }  }
   */  
   /**************** Product of 2 matrices ******************/
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   free_vector(x,1,npar);  {
   free_ivector(indx,1,npar);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   free_matrix(hess,1,npar,1,npar);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
 }       a pointer to pointers identical to out */
     long i, j, k;
 /*************** hessian matrix ****************/    for(i=nrl; i<= nrh; i++)
 double hessii( double x[], double delta, int theta, double delti[])      for(k=ncolol; k<=ncoloh; k++)
 {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   int i;          out[i][k] +=in[i][j]*b[j][k];
   int l=1, lmax=20;  
   double k1,k2;    return out;
   double p2[NPARMAX+1];  }
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;  /************* Higher Matrix Product ***************/
   int k=0,kmax=10;  
   double l1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
   fx=func(x);    /* Computes the transition matrix starting at age 'age' over 
   for (i=1;i<=npar;i++) p2[i]=x[i];       'nhstepm*hstepm*stepm' months (i.e. until
   for(l=0 ; l <=lmax; l++){       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     l1=pow(10,l);       nhstepm*hstepm matrices. 
     delts=delt;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     for(k=1 ; k <kmax; k=k+1){       (typically every 2 years instead of every month which is too big 
       delt = delta*(l1*k);       for the memory).
       p2[theta]=x[theta] +delt;       Model is determined by parameters x and covariates have to be 
       k1=func(p2)-fx;       included manually here. 
       p2[theta]=x[theta]-delt;  
       k2=func(p2)-fx;       */
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    int i, j, d, h, k;
          double **out, cov[NCOVMAX];
 #ifdef DEBUG    double **newm;
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif    /* Hstepm could be zero and should return the unit matrix */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    for (i=1;i<=nlstate+ndeath;i++)
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      for (j=1;j<=nlstate+ndeath;j++){
         k=kmax;        oldm[i][j]=(i==j ? 1.0 : 0.0);
       }        po[i][j][0]=(i==j ? 1.0 : 0.0);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      }
         k=kmax; l=lmax*10.;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       }    for(h=1; h <=nhstepm; h++){
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for(d=1; d <=hstepm; d++){
         delts=delt;        newm=savm;
       }        /* Covariates have to be included here again */
     }        cov[1]=1.;
   }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   delti[theta]=delts;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   return res;        for (k=1; k<=cptcovage;k++)
            cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 }        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {  
   int i;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   int l=1, l1, lmax=20;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double k1,k2,k3,k4,res,fx;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double p2[NPARMAX+1];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   int k;        savm=oldm;
         oldm=newm;
   fx=func(x);      }
   for (k=1; k<=2; k++) {      for(i=1; i<=nlstate+ndeath; i++)
     for (i=1;i<=npar;i++) p2[i]=x[i];        for(j=1;j<=nlstate+ndeath;j++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;          po[i][j][h]=newm[i][j];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     k1=func(p2)-fx;           */
          }
     p2[thetai]=x[thetai]+delti[thetai]/k;    } /* end h */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    return po;
     k2=func(p2)-fx;  }
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*************** log-likelihood *************/
     k3=func(p2)-fx;  double func( double *x)
    {
     p2[thetai]=x[thetai]-delti[thetai]/k;    int i, ii, j, k, mi, d, kk;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     k4=func(p2)-fx;    double **out;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    double sw; /* Sum of weights */
 #ifdef DEBUG    double lli; /* Individual log likelihood */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    int s1, s2;
 #endif    double bbh, survp;
   }    long ipmx;
   return res;    /*extern weight */
 }    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 /************** Inverse of matrix **************/    /*for(i=1;i<imx;i++) 
 void ludcmp(double **a, int n, int *indx, double *d)      printf(" %d\n",s[4][i]);
 {    */
   int i,imax,j,k;    cov[1]=1.;
   double big,dum,sum,temp;  
   double *vv;    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
   vv=vector(1,n);    if(mle==1){
   *d=1.0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (i=1;i<=n;i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     big=0.0;        for(mi=1; mi<= wav[i]-1; mi++){
     for (j=1;j<=n;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       if ((temp=fabs(a[i][j])) > big) big=temp;            for (j=1;j<=nlstate+ndeath;j++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     vv[i]=1.0/big;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   for (j=1;j<=n;j++) {          for(d=0; d<dh[mi][i]; d++){
     for (i=1;i<j;i++) {            newm=savm;
       sum=a[i][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            for (kk=1; kk<=cptcovage;kk++) {
       a[i][j]=sum;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
     big=0.0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=j;i<=n;i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       sum=a[i][j];            savm=oldm;
       for (k=1;k<j;k++)            oldm=newm;
         sum -= a[i][k]*a[k][j];          } /* end mult */
       a[i][j]=sum;        
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         big=dum;          /* But now since version 0.9 we anticipate for bias and large stepm.
         imax=i;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     }           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (j != imax) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for (k=1;k<=n;k++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         dum=a[imax][k];           * probability in order to take into account the bias as a fraction of the way
         a[imax][k]=a[j][k];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         a[j][k]=dum;           * -stepm/2 to stepm/2 .
       }           * For stepm=1 the results are the same as for previous versions of Imach.
       *d = -(*d);           * For stepm > 1 the results are less biased than in previous versions. 
       vv[imax]=vv[j];           */
     }          s1=s[mw[mi][i]][i];
     indx[j]=imax;          s2=s[mw[mi+1][i]][i];
     if (a[j][j] == 0.0) a[j][j]=TINY;          bbh=(double)bh[mi][i]/(double)stepm; 
     if (j != n) {          /* bias is positive if real duration
       dum=1.0/(a[j][j]);           * is higher than the multiple of stepm and negative otherwise.
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           */
     }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   }          if( s2 > nlstate){ 
   free_vector(vv,1,n);  /* Doesn't work */            /* i.e. if s2 is a death state and if the date of death is known then the contribution
 ;               to the likelihood is the probability to die between last step unit time and current 
 }               step unit time, which is also the differences between probability to die before dh 
                and probability to die before dh-stepm . 
 void lubksb(double **a, int n, int *indx, double b[])               In version up to 0.92 likelihood was computed
 {          as if date of death was unknown. Death was treated as any other
   int i,ii=0,ip,j;          health state: the date of the interview describes the actual state
   double sum;          and not the date of a change in health state. The former idea was
            to consider that at each interview the state was recorded
   for (i=1;i<=n;i++) {          (healthy, disable or death) and IMaCh was corrected; but when we
     ip=indx[i];          introduced the exact date of death then we should have modified
     sum=b[ip];          the contribution of an exact death to the likelihood. This new
     b[ip]=b[i];          contribution is smaller and very dependent of the step unit
     if (ii)          stepm. It is no more the probability to die between last interview
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          and month of death but the probability to survive from last
     else if (sum) ii=i;          interview up to one month before death multiplied by the
     b[i]=sum;          probability to die within a month. Thanks to Chris
   }          Jackson for correcting this bug.  Former versions increased
   for (i=n;i>=1;i--) {          mortality artificially. The bad side is that we add another loop
     sum=b[i];          which slows down the processing. The difference can be up to 10%
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          lower mortality.
     b[i]=sum/a[i][i];            */
   }            lli=log(out[s1][s2] - savm[s1][s2]);
 }          }else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 /************ Frequencies ********************/            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)          } 
 {  /* Some frequencies */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   double ***freq; /* Frequencies */          ipmx +=1;
   double *pp;          sw += weight[i];
   double pos, k2, dateintsum=0,k2cpt=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   FILE *ficresp;        } /* end of wave */
   char fileresp[FILENAMELENGTH];      } /* end of individual */
      }  else if(mle==2){
   pp=vector(1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcpy(fileresp,"p");        for(mi=1; mi<= wav[i]-1; mi++){
   strcat(fileresp,fileres);          for (ii=1;ii<=nlstate+ndeath;ii++)
   if((ficresp=fopen(fileresp,"w"))==NULL) {            for (j=1;j<=nlstate+ndeath;j++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     exit(0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          for(d=0; d<=dh[mi][i]; d++){
   j1=0;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   j=cptcoveff;            for (kk=1; kk<=cptcovage;kk++) {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   for(k1=1; k1<=j;k1++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i1=1; i1<=ncodemax[k1];i1++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       j1++;            savm=oldm;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            oldm=newm;
         scanf("%d", i);*/          } /* end mult */
       for (i=-1; i<=nlstate+ndeath; i++)          
         for (jk=-1; jk<=nlstate+ndeath; jk++)            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           for(m=agemin; m <= agemax+3; m++)          /* But now since version 0.9 we anticipate for bias and large stepm.
             freq[i][jk][m]=0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
                 * (in months) between two waves is not a multiple of stepm, we rounded to 
       dateintsum=0;           * the nearest (and in case of equal distance, to the lowest) interval but now
       k2cpt=0;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for (i=1; i<=imx; i++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         bool=1;           * probability in order to take into account the bias as a fraction of the way
         if  (cptcovn>0) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
           for (z1=1; z1<=cptcoveff; z1++)           * -stepm/2 to stepm/2 .
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * For stepm=1 the results are the same as for previous versions of Imach.
               bool=0;           * For stepm > 1 the results are less biased than in previous versions. 
         }           */
         if (bool==1) {          s1=s[mw[mi][i]][i];
           for(m=firstpass; m<=lastpass; m++){          s2=s[mw[mi+1][i]][i];
             k2=anint[m][i]+(mint[m][i]/12.);          bbh=(double)bh[mi][i]/(double)stepm; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          /* bias is positive if real duration
               if(agev[m][i]==0) agev[m][i]=agemax+1;           * is higher than the multiple of stepm and negative otherwise.
               if(agev[m][i]==1) agev[m][i]=agemax+2;           */
               if (m<lastpass) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
               }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                        /*if(lli ==000.0)*/
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                 dateintsum=dateintsum+k2;          ipmx +=1;
                 k2cpt++;          sw += weight[i];
               }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             }        } /* end of wave */
           }      } /* end of individual */
         }    }  else if(mle==3){  /* exponential inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
       if  (cptcovn>0) {            for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficresp, "\n#********** Variable ");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresp, "**********\n#");            }
       }          for(d=0; d<dh[mi][i]; d++){
       for(i=1; i<=nlstate;i++)            newm=savm;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       fprintf(ficresp, "\n");            for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(i=(int)agemin; i <= (int)agemax+3; i++){            }
         if(i==(int)agemax+3)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           printf("Total");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         else            savm=oldm;
           printf("Age %d", i);            oldm=newm;
         for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        
             pp[jk] += freq[jk][m][i];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         }          /* But now since version 0.9 we anticipate for bias and large stepm.
         for(jk=1; jk <=nlstate ; jk++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           for(m=-1, pos=0; m <=0 ; m++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
             pos += freq[jk][m][i];           * the nearest (and in case of equal distance, to the lowest) interval but now
           if(pp[jk]>=1.e-10)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
           else           * probability in order to take into account the bias as a fraction of the way
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         }           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
         for(jk=1; jk <=nlstate ; jk++){           * For stepm > 1 the results are less biased than in previous versions. 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)           */
             pp[jk] += freq[jk][m][i];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
         for(jk=1,pos=0; jk <=nlstate ; jk++)          /* bias is positive if real duration
           pos += pp[jk];           * is higher than the multiple of stepm and negative otherwise.
         for(jk=1; jk <=nlstate ; jk++){           */
           if(pos>=1.e-5)          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           else          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          /*if(lli ==000.0)*/
           if( i <= (int) agemax){          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
             if(pos>=1.e-5){          ipmx +=1;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          sw += weight[i];
               probs[i][jk][j1]= pp[jk]/pos;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        } /* end of wave */
             }      } /* end of individual */
             else    }else if (mle==4){  /* ml=4 no inter-extrapolation */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
                  for (ii=1;ii<=nlstate+ndeath;ii++)
         for(jk=-1; jk <=nlstate+ndeath; jk++)            for (j=1;j<=nlstate+ndeath;j++){
           for(m=-1; m <=nlstate+ndeath; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if(i <= (int) agemax)            }
           fprintf(ficresp,"\n");          for(d=0; d<dh[mi][i]; d++){
         printf("\n");            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   dateintmean=dateintsum/k2cpt;            }
            
   fclose(ficresp);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(pp,1,nlstate);            savm=oldm;
              oldm=newm;
   /* End of Freq */          } /* end mult */
 }        
           s1=s[mw[mi][i]][i];
 /************ Prevalence ********************/          s2=s[mw[mi+1][i]][i];
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)          if( s2 > nlstate){ 
 {  /* Some frequencies */            lli=log(out[s1][s2] - savm[s1][s2]);
            }else{
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double ***freq; /* Frequencies */          }
   double *pp;          ipmx +=1;
   double pos, k2;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   pp=vector(1,nlstate);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        } /* end of wave */
        } /* end of individual */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   j1=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   j=cptcoveff;        for(mi=1; mi<= wav[i]-1; mi++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
  for(k1=1; k1<=j;k1++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i1=1; i1<=ncodemax[k1];i1++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       j1++;            }
            for(d=0; d<dh[mi][i]; d++){
       for (i=-1; i<=nlstate+ndeath; i++)              newm=savm;
         for (jk=-1; jk<=nlstate+ndeath; jk++)              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=agemin; m <= agemax+3; m++)            for (kk=1; kk<=cptcovage;kk++) {
             freq[i][jk][m]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                  }
       for (i=1; i<=imx; i++) {          
         bool=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         if  (cptcovn>0) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for (z1=1; z1<=cptcoveff; z1++)            savm=oldm;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            oldm=newm;
               bool=0;          } /* end mult */
         }        
         if (bool==1) {          s1=s[mw[mi][i]][i];
           for(m=firstpass; m<=lastpass; m++){          s2=s[mw[mi+1][i]][i];
             k2=anint[m][i]+(mint[m][i]/12.);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          ipmx +=1;
               if(agev[m][i]==0) agev[m][i]=agemax+1;          sw += weight[i];
               if(agev[m][i]==1) agev[m][i]=agemax+2;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */        } /* end of wave */
             }      } /* end of individual */
           }    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         for(i=(int)agemin; i <= (int)agemax+3; i++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           for(jk=1; jk <=nlstate ; jk++){    return -l;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  }
               pp[jk] += freq[jk][m][i];  
           }  /*************** log-likelihood *************/
           for(jk=1; jk <=nlstate ; jk++){  double funcone( double *x)
             for(m=-1, pos=0; m <=0 ; m++)  {
             pos += freq[jk][m][i];    /* Same as likeli but slower because of a lot of printf and if */
         }    int i, ii, j, k, mi, d, kk;
            double l, ll[NLSTATEMAX], cov[NCOVMAX];
          for(jk=1; jk <=nlstate ; jk++){    double **out;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double lli; /* Individual log likelihood */
              pp[jk] += freq[jk][m][i];    double llt;
          }    int s1, s2;
              double bbh, survp;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    /*extern weight */
     /* We are differentiating ll according to initial status */
          for(jk=1; jk <=nlstate ; jk++){              /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
            if( i <= (int) agemax){    /*for(i=1;i<imx;i++) 
              if(pos>=1.e-5){      printf(" %d\n",s[4][i]);
                probs[i][jk][j1]= pp[jk]/pos;    */
              }    cov[1]=1.;
            }  
          }    for(k=1; k<=nlstate; k++) ll[k]=0.;
            
         }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }      for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(pp,1,nlstate);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
            }
 }  /* End of Freq */        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
 /************* Waves Concatenation ***************/          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {          }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      Death is a valid wave (if date is known).                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          savm=oldm;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          oldm=newm;
      and mw[mi+1][i]. dh depends on stepm.        } /* end mult */
      */        
         s1=s[mw[mi][i]][i];
   int i, mi, m;        s2=s[mw[mi+1][i]][i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        bbh=(double)bh[mi][i]/(double)stepm; 
      double sum=0., jmean=0.;*/        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
   int j, k=0,jk, ju, jl;         */
   double sum=0.;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   jmin=1e+5;          lli=log(out[s1][s2] - savm[s1][s2]);
   jmax=-1;        } else if (mle==1){
   jmean=0.;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for(i=1; i<=imx; i++){        } else if(mle==2){
     mi=0;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     m=firstpass;        } else if(mle==3){  /* exponential inter-extrapolation */
     while(s[m][i] <= nlstate){          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       if(s[m][i]>=1)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         mw[++mi][i]=m;          lli=log(out[s1][s2]); /* Original formula */
       if(m >=lastpass)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         break;          lli=log(out[s1][s2]); /* Original formula */
       else        } /* End of if */
         m++;        ipmx +=1;
     }/* end while */        sw += weight[i];
     if (s[m][i] > nlstate){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       mi++;     /* Death is another wave */  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       /* if(mi==0)  never been interviewed correctly before death */        if(globpr){
          /* Only death is a correct wave */          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
       mw[mi][i]=m;   %10.6f %10.6f %10.6f ", \
     }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     wav[i]=mi;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     if(mi==0)            llt +=ll[k]*gipmx/gsw;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   }          }
           fprintf(ficresilk," %10.6f\n", -llt);
   for(i=1; i<=imx; i++){        }
     for(mi=1; mi<wav[i];mi++){      } /* end of wave */
       if (stepm <=0)    } /* end of individual */
         dh[mi][i]=1;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       else{    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         if (s[mw[mi+1][i]][i] > nlstate) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           if (agedc[i] < 2*AGESUP) {    if(globpr==0){ /* First time we count the contributions and weights */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      gipmx=ipmx;
           if(j==0) j=1;  /* Survives at least one month after exam */      gsw=sw;
           k=k+1;    }
           if (j >= jmax) jmax=j;    return -l;
           if (j <= jmin) jmin=j;  }
           sum=sum+j;  
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  char *subdirf(char fileres[])
           }  {
         }    /* Caution optionfilefiname is hidden */
         else{    strcpy(tmpout,optionfilefiname);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    strcat(tmpout,"/"); /* Add to the right */
           k=k+1;    strcat(tmpout,fileres);
           if (j >= jmax) jmax=j;    return tmpout;
           else if (j <= jmin)jmin=j;  }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  
           sum=sum+j;  char *subdirf2(char fileres[], char *preop)
         }  {
         jk= j/stepm;    
         jl= j -jk*stepm;    strcpy(tmpout,optionfilefiname);
         ju= j -(jk+1)*stepm;    strcat(tmpout,"/");
         if(jl <= -ju)    strcat(tmpout,preop);
           dh[mi][i]=jk;    strcat(tmpout,fileres);
         else    return tmpout;
           dh[mi][i]=jk+1;  }
         if(dh[mi][i]==0)  char *subdirf3(char fileres[], char *preop, char *preop2)
           dh[mi][i]=1; /* At least one step */  {
       }    
     }    strcpy(tmpout,optionfilefiname);
   }    strcat(tmpout,"/");
   jmean=sum/k;    strcat(tmpout,preop);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    strcat(tmpout,preop2);
  }    strcat(tmpout,fileres);
 /*********** Tricode ****************************/    return tmpout;
 void tricode(int *Tvar, int **nbcode, int imx)  }
 {  
   int Ndum[20],ij=1, k, j, i;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   int cptcode=0;  {
   cptcoveff=0;    /* This routine should help understanding what is done with 
         the selection of individuals/waves and
   for (k=0; k<19; k++) Ndum[k]=0;       to check the exact contribution to the likelihood.
   for (k=1; k<=7; k++) ncodemax[k]=0;       Plotting could be done.
      */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    int k;
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);    if(*globpri !=0){ /* Just counts and sums, no printings */
       Ndum[ij]++;      strcpy(fileresilk,"ilk"); 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      strcat(fileresilk,fileres);
       if (ij > cptcode) cptcode=ij;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     }        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     for (i=0; i<=cptcode; i++) {      }
       if(Ndum[i]!=0) ncodemax[j]++;      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     ij=1;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     for (i=1; i<=ncodemax[j]; i++) {      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       for (k=0; k<=19; k++) {    }
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;    *fretone=(*funcone)(p);
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/    if(*globpri !=0){
           ij++;      fclose(ficresilk);
         }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         if (ij > ncodemax[j]) break;      fflush(fichtm); 
       }      } 
     }    return;
   }    }
   
  for (k=0; k<19; k++) Ndum[k]=0;  
   /*********** Maximum Likelihood Estimation ***************/
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       Ndum[ij]++;  {
     }    int i,j, iter;
     double **xi;
  ij=1;    double fret;
  for (i=1; i<=10; i++) {    double fretone; /* Only one call to likelihood */
    if((Ndum[i]!=0) && (i<=ncovcol)){    char filerespow[FILENAMELENGTH];
      Tvaraff[ij]=i;    xi=matrix(1,npar,1,npar);
      ij++;    for (i=1;i<=npar;i++)
    }      for (j=1;j<=npar;j++)
  }        xi[i][j]=(i==j ? 1.0 : 0.0);
      printf("Powell\n");  fprintf(ficlog,"Powell\n");
     cptcoveff=ij-1;    strcpy(filerespow,"pow"); 
 }    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
 /*********** Health Expectancies ****************/      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)    }
 {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   /* Health expectancies */    for (i=1;i<=nlstate;i++)
   int i, j, nhstepm, hstepm, h, nstepm;      for(j=1;j<=nlstate+ndeath;j++)
   double age, agelim, hf;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double ***p3mat;    fprintf(ficrespow,"\n");
    
   fprintf(ficreseij,"# Health expectancies\n");    powell(p,xi,npar,ftol,&iter,&fret,func);
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)    fclose(ficrespow);
     for(j=1; j<=nlstate;j++)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       fprintf(ficreseij," %1d-%1d",i,j);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fprintf(ficreseij,"\n");    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
   if(estepm < stepm){  }
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }  /**** Computes Hessian and covariance matrix ***/
   else  hstepm=estepm;    void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   /* We compute the life expectancy from trapezoids spaced every estepm months  {
    * This is mainly to measure the difference between two models: for example    double  **a,**y,*x,pd;
    * if stepm=24 months pijx are given only every 2 years and by summing them    double **hess;
    * we are calculating an estimate of the Life Expectancy assuming a linear    int i, j,jk;
    * progression inbetween and thus overestimating or underestimating according    int *indx;
    * to the curvature of the survival function. If, for the same date, we  
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    double hessii(double p[], double delta, int theta, double delti[]);
    * to compare the new estimate of Life expectancy with the same linear    double hessij(double p[], double delti[], int i, int j);
    * hypothesis. A more precise result, taking into account a more precise    void lubksb(double **a, int npar, int *indx, double b[]) ;
    * curvature will be obtained if estepm is as small as stepm. */    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
   /* For example we decided to compute the life expectancy with the smallest unit */    hess=matrix(1,npar,1,npar);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  
      nhstepm is the number of hstepm from age to agelim    printf("\nCalculation of the hessian matrix. Wait...\n");
      nstepm is the number of stepm from age to agelin.    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
      Look at hpijx to understand the reason of that which relies in memory size    for (i=1;i<=npar;i++){
      and note for a fixed period like estepm months */      printf("%d",i);fflush(stdout);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      fprintf(ficlog,"%d",i);fflush(ficlog);
      survival function given by stepm (the optimization length). Unfortunately it      hess[i][i]=hessii(p,ftolhess,i,delti);
      means that if the survival funtion is printed only each two years of age and if      /*printf(" %f ",p[i]);*/
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      /*printf(" %lf ",hess[i][i]);*/
      results. So we changed our mind and took the option of the best precision.    }
   */    
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
   agelim=AGESUP;        if (j>i) { 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          printf(".%d%d",i,j);fflush(stdout);
     /* nhstepm age range expressed in number of stepm */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          hess[i][j]=hessij(p,delti,i,j);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          hess[j][i]=hess[i][j];    
     /* if (stepm >= YEARM) hstepm=1;*/          /*printf(" %lf ",hess[i][j]);*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    printf("\n");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      fprintf(ficlog,"\n");
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(i=1; i<=nlstate;i++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(j=1; j<=nlstate;j++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    a=matrix(1,npar,1,npar);
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    y=matrix(1,npar,1,npar);
         }    x=vector(1,npar);
     fprintf(ficreseij,"%3.0f",age );    indx=ivector(1,npar);
     for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++)
       for(j=1; j<=nlstate;j++){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    ludcmp(a,npar,indx,&pd);
       }  
     fprintf(ficreseij,"\n");    for (j=1;j<=npar;j++) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1;i<=npar;i++) x[i]=0;
   }      x[j]=1;
 }      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 /************ Variance ******************/        matcov[i][j]=x[i];
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)      }
 {    }
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    printf("\n#Hessian matrix#\n");
   double **newm;    fprintf(ficlog,"\n#Hessian matrix#\n");
   double **dnewm,**doldm;    for (i=1;i<=npar;i++) { 
   int i, j, nhstepm, hstepm, h, nstepm ;      for (j=1;j<=npar;j++) { 
   int k, cptcode;        printf("%.3e ",hess[i][j]);
   double *xp;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double **gp, **gm;      }
   double ***gradg, ***trgradg;      printf("\n");
   double ***p3mat;      fprintf(ficlog,"\n");
   double age,agelim, hf;    }
   int theta;  
     /* Recompute Inverse */
    fprintf(ficresvij,"# Covariances of life expectancies\n");    for (i=1;i<=npar;i++)
   fprintf(ficresvij,"# Age");      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   for(i=1; i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    /*  printf("\n#Hessian matrix recomputed#\n");
   fprintf(ficresvij,"\n");  
     for (j=1;j<=npar;j++) {
   xp=vector(1,npar);      for (i=1;i<=npar;i++) x[i]=0;
   dnewm=matrix(1,nlstate,1,npar);      x[j]=1;
   doldm=matrix(1,nlstate,1,nlstate);      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   if(estepm < stepm){        y[i][j]=x[i];
     printf ("Problem %d lower than %d\n",estepm, stepm);        printf("%.3e ",y[i][j]);
   }        fprintf(ficlog,"%.3e ",y[i][j]);
   else  hstepm=estepm;        }
   /* For example we decided to compute the life expectancy with the smallest unit */      printf("\n");
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      fprintf(ficlog,"\n");
      nhstepm is the number of hstepm from age to agelim    }
      nstepm is the number of stepm from age to agelin.    */
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */    free_matrix(a,1,npar,1,npar);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    free_matrix(y,1,npar,1,npar);
      survival function given by stepm (the optimization length). Unfortunately it    free_vector(x,1,npar);
      means that if the survival funtion is printed only each two years of age and if    free_ivector(indx,1,npar);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    free_matrix(hess,1,npar,1,npar);
      results. So we changed our mind and took the option of the best precision.  
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  }
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /*************** hessian matrix ****************/
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  double hessii( double x[], double delta, int theta, double delti[])
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    int l=1, lmax=20;
     gp=matrix(0,nhstepm,1,nlstate);    double k1,k2;
     gm=matrix(0,nhstepm,1,nlstate);    double p2[NPARMAX+1];
     double res;
     for(theta=1; theta <=npar; theta++){    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double fx;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int k=0,kmax=10;
       }    double l1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
       if (popbased==1) {    for(l=0 ; l <=lmax; l++){
         for(i=1; i<=nlstate;i++)      l1=pow(10,l);
           prlim[i][i]=probs[(int)age][i][ij];      delts=delt;
       }      for(k=1 ; k <kmax; k=k+1){
          delt = delta*(l1*k);
       for(j=1; j<= nlstate; j++){        p2[theta]=x[theta] +delt;
         for(h=0; h<=nhstepm; h++){        k1=func(p2)-fx;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        p2[theta]=x[theta]-delt;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        k2=func(p2)-fx;
         }        /*res= (k1-2.0*fx+k2)/delt/delt; */
       }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
            
       for(i=1; i<=npar; i++) /* Computes gradient */  #ifdef DEBUG
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  #endif
          /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       if (popbased==1) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for(i=1; i<=nlstate;i++)          k=kmax;
           prlim[i][i]=probs[(int)age][i][ij];        }
       }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
       for(j=1; j<= nlstate; j++){        }
         for(h=0; h<=nhstepm; h++){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          delts=delt;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        }
         }      }
       }    }
     delti[theta]=delts;
       for(j=1; j<= nlstate; j++)    return res; 
         for(h=0; h<=nhstepm; h++){    
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  }
         }  
     } /* End theta */  double hessij( double x[], double delti[], int thetai,int thetaj)
   {
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    int i;
     int l=1, l1, lmax=20;
     for(h=0; h<=nhstepm; h++)    double k1,k2,k3,k4,res,fx;
       for(j=1; j<=nlstate;j++)    double p2[NPARMAX+1];
         for(theta=1; theta <=npar; theta++)    int k;
           trgradg[h][j][theta]=gradg[h][theta][j];  
     fx=func(x);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    for (k=1; k<=2; k++) {
     for(i=1;i<=nlstate;i++)      for (i=1;i<=npar;i++) p2[i]=x[i];
       for(j=1;j<=nlstate;j++)      p2[thetai]=x[thetai]+delti[thetai]/k;
         vareij[i][j][(int)age] =0.;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
     for(h=0;h<=nhstepm;h++){    
       for(k=0;k<=nhstepm;k++){      p2[thetai]=x[thetai]+delti[thetai]/k;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      k2=func(p2)-fx;
         for(i=1;i<=nlstate;i++)    
           for(j=1;j<=nlstate;j++)      p2[thetai]=x[thetai]-delti[thetai]/k;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k3=func(p2)-fx;
     }    
       p2[thetai]=x[thetai]-delti[thetai]/k;
     fprintf(ficresvij,"%.0f ",age );      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(i=1; i<=nlstate;i++)      k4=func(p2)-fx;
       for(j=1; j<=nlstate;j++){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  #ifdef DEBUG
       }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     fprintf(ficresvij,"\n");      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     free_matrix(gp,0,nhstepm,1,nlstate);  #endif
     free_matrix(gm,0,nhstepm,1,nlstate);    }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    return res;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */  /************** Inverse of matrix **************/
    void ludcmp(double **a, int n, int *indx, double *d) 
   free_vector(xp,1,npar);  { 
   free_matrix(doldm,1,nlstate,1,npar);    int i,imax,j,k; 
   free_matrix(dnewm,1,nlstate,1,nlstate);    double big,dum,sum,temp; 
     double *vv; 
 }   
     vv=vector(1,n); 
 /************ Variance of prevlim ******************/    *d=1.0; 
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    for (i=1;i<=n;i++) { 
 {      big=0.0; 
   /* Variance of prevalence limit */      for (j=1;j<=n;j++) 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        if ((temp=fabs(a[i][j])) > big) big=temp; 
   double **newm;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   double **dnewm,**doldm;      vv[i]=1.0/big; 
   int i, j, nhstepm, hstepm;    } 
   int k, cptcode;    for (j=1;j<=n;j++) { 
   double *xp;      for (i=1;i<j;i++) { 
   double *gp, *gm;        sum=a[i][j]; 
   double **gradg, **trgradg;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double age,agelim;        a[i][j]=sum; 
   int theta;      } 
          big=0.0; 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      for (i=j;i<=n;i++) { 
   fprintf(ficresvpl,"# Age");        sum=a[i][j]; 
   for(i=1; i<=nlstate;i++)        for (k=1;k<j;k++) 
       fprintf(ficresvpl," %1d-%1d",i,i);          sum -= a[i][k]*a[k][j]; 
   fprintf(ficresvpl,"\n");        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
   xp=vector(1,npar);          big=dum; 
   dnewm=matrix(1,nlstate,1,npar);          imax=i; 
   doldm=matrix(1,nlstate,1,nlstate);        } 
        } 
   hstepm=1*YEARM; /* Every year of age */      if (j != imax) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for (k=1;k<=n;k++) { 
   agelim = AGESUP;          dum=a[imax][k]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          a[imax][k]=a[j][k]; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          a[j][k]=dum; 
     if (stepm >= YEARM) hstepm=1;        } 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        *d = -(*d); 
     gradg=matrix(1,npar,1,nlstate);        vv[imax]=vv[j]; 
     gp=vector(1,nlstate);      } 
     gm=vector(1,nlstate);      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
     for(theta=1; theta <=npar; theta++){      if (j != n) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */        dum=1.0/(a[j][j]); 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       }      } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } 
       for(i=1;i<=nlstate;i++)    free_vector(vv,1,n);  /* Doesn't work */
         gp[i] = prlim[i][i];  ;
      } 
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  void lubksb(double **a, int n, int *indx, double b[]) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  { 
       for(i=1;i<=nlstate;i++)    int i,ii=0,ip,j; 
         gm[i] = prlim[i][i];    double sum; 
    
       for(i=1;i<=nlstate;i++)    for (i=1;i<=n;i++) { 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      ip=indx[i]; 
     } /* End theta */      sum=b[ip]; 
       b[ip]=b[i]; 
     trgradg =matrix(1,nlstate,1,npar);      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     for(j=1; j<=nlstate;j++)      else if (sum) ii=i; 
       for(theta=1; theta <=npar; theta++)      b[i]=sum; 
         trgradg[j][theta]=gradg[theta][j];    } 
     for (i=n;i>=1;i--) { 
     for(i=1;i<=nlstate;i++)      sum=b[i]; 
       varpl[i][(int)age] =0.;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      b[i]=sum/a[i][i]; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    } 
     for(i=1;i<=nlstate;i++)  } 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
   /************ Frequencies ********************/
     fprintf(ficresvpl,"%.0f ",age );  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
     for(i=1; i<=nlstate;i++)  {  /* Some frequencies */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    
     fprintf(ficresvpl,"\n");    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     free_vector(gp,1,nlstate);    int first;
     free_vector(gm,1,nlstate);    double ***freq; /* Frequencies */
     free_matrix(gradg,1,npar,1,nlstate);    double *pp, **prop;
     free_matrix(trgradg,1,nlstate,1,npar);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   } /* End age */    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
   free_vector(xp,1,npar);    
   free_matrix(doldm,1,nlstate,1,npar);    pp=vector(1,nlstate);
   free_matrix(dnewm,1,nlstate,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
 }    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
 /************ Variance of one-step probabilities  ******************/      printf("Problem with prevalence resultfile: %s\n", fileresp);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 {      exit(0);
   int i, j;    }
   int k=0, cptcode;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   double **dnewm,**doldm;    j1=0;
   double *xp;    
   double *gp, *gm;    j=cptcoveff;
   double **gradg, **trgradg;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   double age,agelim, cov[NCOVMAX];  
   int theta;    first=1;
   char fileresprob[FILENAMELENGTH];  
     for(k1=1; k1<=j;k1++){
   strcpy(fileresprob,"prob");      for(i1=1; i1<=ncodemax[k1];i1++){
   strcat(fileresprob,fileres);        j1++;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     printf("Problem with resultfile: %s\n", fileresprob);          scanf("%d", i);*/
   }        for (i=-1; i<=nlstate+ndeath; i++)  
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
              for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (i=1; i<=nlstate; i++)  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        for(m=iagemin; m <= iagemax+3; m++)
            prop[i][m]=0;
   cov[1]=1;        
   for (age=bage; age<=fage; age ++){        dateintsum=0;
     cov[2]=age;        k2cpt=0;
     gradg=matrix(1,npar,1,9);        for (i=1; i<=imx; i++) {
     trgradg=matrix(1,9,1,npar);          bool=1;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          if  (cptcovn>0) {
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            for (z1=1; z1<=cptcoveff; z1++) 
                  if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for(theta=1; theta <=npar; theta++){                bool=0;
       for(i=1; i<=npar; i++)          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          if (bool==1){
                  for(m=firstpass; m<=lastpass; m++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              k2=anint[m][i]+(mint[m][i]/12.);
                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       k=0;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for(i=1; i<= (nlstate+ndeath); i++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         for(j=1; j<=(nlstate+ndeath);j++){                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
            k=k+1;                if (m<lastpass) {
           gp[k]=pmmij[i][j];                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       }                }
                 
       for(i=1; i<=npar; i++)                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                  dateintsum=dateintsum+k2;
                      k2cpt++;
                 }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);                /*}*/
       k=0;            }
       for(i=1; i<=(nlstate+ndeath); i++){          }
         for(j=1; j<=(nlstate+ndeath);j++){        }
           k=k+1;         
           gm[k]=pmmij[i][j];        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         }  
       }        if  (cptcovn>0) {
                fprintf(ficresp, "\n#********** Variable "); 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            fprintf(ficresp, "**********\n#");
     }        }
         for(i=1; i<=nlstate;i++) 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       for(theta=1; theta <=npar; theta++)        fprintf(ficresp, "\n");
       trgradg[j][theta]=gradg[theta][j];        
          for(i=iagemin; i <= iagemax+3; i++){
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          if(i==iagemax+3){
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);            fprintf(ficlog,"Total");
           }else{
      pmij(pmmij,cov,ncovmodel,x,nlstate);            if(first==1){
               first=0;
      k=0;              printf("See log file for details...\n");
      for(i=1; i<=(nlstate+ndeath); i++){            }
        for(j=1; j<=(nlstate+ndeath);j++){            fprintf(ficlog,"Age %d", i);
          k=k+1;          }
          gm[k]=pmmij[i][j];          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      }              pp[jk] += freq[jk][m][i]; 
                }
      /*printf("\n%d ",(int)age);          for(jk=1; jk <=nlstate ; jk++){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            for(m=-1, pos=0; m <=0 ; m++)
                      pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              if(first==1){
      }*/              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
   fprintf(ficresprob,"\n%d ",(int)age);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              if(first==1)
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   }            }
           }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          for(jk=1; jk <=nlstate ; jk++){
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              pp[jk] += freq[jk][m][i];
 }          }       
  free_vector(xp,1,npar);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 fclose(ficresprob);            pos += pp[jk];
             posprop += prop[jk][i];
 }          }
           for(jk=1; jk <=nlstate ; jk++){
 /******************* Printing html file ***********/            if(pos>=1.e-5){
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \              if(first==1)
  int lastpass, int stepm, int weightopt, char model[],\                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\            }else{
  char version[], int popforecast, int estepm ){              if(first==1)
   int jj1, k1, i1, cpt;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   FILE *fichtm;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /*char optionfilehtm[FILENAMELENGTH];*/            }
             if( i <= iagemax){
   strcpy(optionfilehtm,optionfile);              if(pos>=1.e-5){
   strcat(optionfilehtm,".htm");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                /*probs[i][jk][j1]= pp[jk]/pos;*/
     printf("Problem with %s \n",optionfilehtm), exit(0);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   }              }
               else
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n            }
 \n          }
 Total number of observations=%d <br>\n          
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n          for(jk=-1; jk <=nlstate+ndeath; jk++)
 <hr  size=\"2\" color=\"#EC5E5E\">            for(m=-1; m <=nlstate+ndeath; m++)
  <ul><li>Outputs files<br>\n              if(freq[jk][m][i] !=0 ) {
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n              if(first==1)
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n              }
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n          if(i <= iagemax)
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);            fprintf(ficresp,"\n");
           if(first==1)
  fprintf(fichtm,"\n            printf("Others in log...\n");
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n          fprintf(ficlog,"\n");
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        }
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      }
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    }
     dateintmean=dateintsum/k2cpt; 
  if(popforecast==1) fprintf(fichtm,"\n   
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    fclose(ficresp);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
         <br>",fileres,fileres,fileres,fileres);    free_vector(pp,1,nlstate);
  else    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    /* End of Freq */
 fprintf(fichtm," <li>Graphs</li><p>");  }
   
  m=cptcoveff;  /************ Prevalence ********************/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
  jj1=0;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
  for(k1=1; k1<=m;k1++){       in each health status at the date of interview (if between dateprev1 and dateprev2).
    for(i1=1; i1<=ncodemax[k1];i1++){       We still use firstpass and lastpass as another selection.
        jj1++;    */
        if (cptcovn > 0) {   
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
          for (cpt=1; cpt<=cptcoveff;cpt++)    double ***freq; /* Frequencies */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double *pp, **prop;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double pos,posprop; 
        }    double  y2; /* in fractional years */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    int iagemin, iagemax;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      
        for(cpt=1; cpt<nlstate;cpt++){    iagemin= (int) agemin;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    iagemax= (int) agemax;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /*pp=vector(1,nlstate);*/
        }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     for(cpt=1; cpt<=nlstate;cpt++) {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    j1=0;
 interval) in state (%d): v%s%d%d.gif <br>    
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      j=cptcoveff;
      }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      for(cpt=1; cpt<=nlstate;cpt++) {    
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    for(k1=1; k1<=j;k1++){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for(i1=1; i1<=ncodemax[k1];i1++){
      }        j1++;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        
 health expectancies in states (1) and (2): e%s%d.gif<br>        for (i=1; i<=nlstate; i++)  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for(m=iagemin; m <= iagemax+3; m++)
 fprintf(fichtm,"\n</body>");            prop[i][m]=0.0;
    }       
    }        for (i=1; i<=imx; i++) { /* Each individual */
 fclose(fichtm);          bool=1;
 }          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
 /******************* Gnuplot file **************/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){                bool=0;
           } 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   strcpy(optionfilegnuplot,optionfilefiname);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   strcat(optionfilegnuplot,".gp.txt");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     printf("Problem with file %s",optionfilegnuplot);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
 #ifdef windows                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     fprintf(ficgp,"cd \"%s\" \n",pathc);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 #endif                  prop[s[m][i]][iagemax+3] += weight[i]; 
 m=pow(2,cptcoveff);                } 
                }
  /* 1eme*/            } /* end selection of waves */
   for (cpt=1; cpt<= nlstate ; cpt ++) {          }
    for (k1=1; k1<= m ; k1 ++) {        }
         for(i=iagemin; i <= iagemax+3; i++){  
 #ifdef windows          
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 #endif            posprop += prop[jk][i]; 
 #ifdef unix          } 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
 for (i=1; i<= nlstate ; i ++) {              if(posprop>=1.e-5){ 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                probs[i][jk][j1]= prop[jk][i]/posprop;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              } 
 }            } 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          }/* end jk */ 
     for (i=1; i<= nlstate ; i ++) {        }/* end i */ 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      } /* end i1 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    } /* end k1 */
 }    
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      for (i=1; i<= nlstate ; i ++) {    /*free_vector(pp,1,nlstate);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }  /* End of prevalence */
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  /************* Waves Concatenation ***************/
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 #endif  {
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
    }       Death is a valid wave (if date is known).
   }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   /*2 eme*/       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
   for (k1=1; k1<= m ; k1 ++) {       */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);  
        int i, mi, m;
     for (i=1; i<= nlstate+1 ; i ++) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       k=2*i;       double sum=0., jmean=0.;*/
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    int first;
       for (j=1; j<= nlstate+1 ; j ++) {    int j, k=0,jk, ju, jl;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double sum=0.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    first=0;
 }      jmin=1e+5;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    jmax=-1;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    jmean=0.;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    for(i=1; i<=imx; i++){
       for (j=1; j<= nlstate+1 ; j ++) {      mi=0;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      m=firstpass;
         else fprintf(ficgp," \%%*lf (\%%*lf)");      while(s[m][i] <= nlstate){
 }          if(s[m][i]>=1)
       fprintf(ficgp,"\" t\"\" w l 0,");          mw[++mi][i]=m;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        if(m >=lastpass)
       for (j=1; j<= nlstate+1 ; j ++) {          break;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        else
   else fprintf(ficgp," \%%*lf (\%%*lf)");          m++;
 }        }/* end while */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      if (s[m][i] > nlstate){
       else fprintf(ficgp,"\" t\"\" w l 0,");        mi++;     /* Death is another wave */
     }        /* if(mi==0)  never been interviewed correctly before death */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);           /* Only death is a correct wave */
   }        mw[mi][i]=m;
        }
   /*3eme*/  
       wav[i]=mi;
   for (k1=1; k1<= m ; k1 ++) {      if(mi==0){
     for (cpt=1; cpt<= nlstate ; cpt ++) {        nbwarn++;
       k=2+nlstate*(cpt-1);        if(first==0){
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       for (i=1; i< nlstate ; i ++) {          first=1;
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        }
       }        if(first==1){
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     }        }
     }      } /* end mi==0 */
      } /* End individuals */
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {    for(i=1; i<=imx; i++){
     for (cpt=1; cpt<nlstate ; cpt ++) {      for(mi=1; mi<wav[i];mi++){
       k=3;        if (stepm <=0)
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          dh[mi][i]=1;
         else{
       for (i=1; i< nlstate ; i ++)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         fprintf(ficgp,"+$%d",k+i+1);            if (agedc[i] < 2*AGESUP) {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                    if(j==0) j=1;  /* Survives at least one month after exam */
       l=3+(nlstate+ndeath)*cpt;              else if(j<0){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                nberr++;
       for (i=1; i< nlstate ; i ++) {                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         l=3+(nlstate+ndeath)*cpt;                j=1; /* Temporary Dangerous patch */
         fprintf(ficgp,"+$%d",l+i+1);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
       }                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              }
     }              k=k+1;
   }                if (j >= jmax) jmax=j;
                if (j <= jmin) jmin=j;
   /* proba elementaires */              sum=sum+j;
    for(i=1,jk=1; i <=nlstate; i++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     for(k=1; k <=(nlstate+ndeath); k++){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       if (k != i) {            }
         for(j=1; j <=ncovmodel; j++){          }
                  else{
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           jk++;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           fprintf(ficgp,"\n");            k=k+1;
         }            if (j >= jmax) jmax=j;
       }            else if (j <= jmin)jmin=j;
     }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
     for(jk=1; jk <=m; jk++) {              nberr++;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    i=1;              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    for(k2=1; k2<=nlstate; k2++) {            }
      k3=i;            sum=sum+j;
      for(k=1; k<=(nlstate+ndeath); k++) {          }
        if (k != k2){          jk= j/stepm;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          jl= j -jk*stepm;
 ij=1;          ju= j -(jk+1)*stepm;
         for(j=3; j <=ncovmodel; j++) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            if(jl==0){
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              dh[mi][i]=jk;
             ij++;              bh[mi][i]=0;
           }            }else{ /* We want a negative bias in order to only have interpolation ie
           else                    * at the price of an extra matrix product in likelihood */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              dh[mi][i]=jk+1;
         }              bh[mi][i]=ju;
           fprintf(ficgp,")/(1");            }
                  }else{
         for(k1=1; k1 <=nlstate; k1++){              if(jl <= -ju){
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              dh[mi][i]=jk;
 ij=1;              bh[mi][i]=jl;       /* bias is positive if real duration
           for(j=3; j <=ncovmodel; j++){                                   * is higher than the multiple of stepm and negative otherwise.
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                                   */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            }
             ij++;            else{
           }              dh[mi][i]=jk+1;
           else              bh[mi][i]=ju;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            }
           }            if(dh[mi][i]==0){
           fprintf(ficgp,")");              dh[mi][i]=1; /* At least one step */
         }              bh[mi][i]=ju; /* At least one step */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            }
         i=i+ncovmodel;          } /* end if mle */
        }        }
      }      } /* end wave */
    }    }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    jmean=sum/k;
    }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
        fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   fclose(ficgp);   }
 }  /* end gnuplot */  
   /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
 /*************** Moving average **************/  {
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
   int i, cpt, cptcod;    int cptcode=0;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    cptcoveff=0; 
       for (i=1; i<=nlstate;i++)   
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    for (k=0; k<maxncov; k++) Ndum[k]=0;
           mobaverage[(int)agedeb][i][cptcod]=0.;    for (k=1; k<=7; k++) ncodemax[k]=0;
      
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=nlstate;i++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                                 modality*/ 
           for (cpt=0;cpt<=4;cpt++){        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        Ndum[ij]++; /*store the modality */
           }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         }                                         Tvar[j]. If V=sex and male is 0 and 
       }                                         female is 1, then  cptcode=1.*/
     }      }
      
 }      for (i=0; i<=cptcode; i++) {
         if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       }
 /************** Forecasting ******************/  
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){      ij=1; 
        for (i=1; i<=ncodemax[j]; i++) {
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for (k=0; k<= maxncov; k++) {
   int *popage;          if (Ndum[k] != 0) {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            nbcode[Tvar[j]][ij]=k; 
   double *popeffectif,*popcount;            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   double ***p3mat;            
   char fileresf[FILENAMELENGTH];            ij++;
           }
  agelim=AGESUP;          if (ij > ncodemax[j]) break; 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        }  
       } 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    }  
    
     for (k=0; k< maxncov; k++) Ndum[k]=0;
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);   for (i=1; i<=ncovmodel-2; i++) { 
   if((ficresf=fopen(fileresf,"w"))==NULL) {     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     printf("Problem with forecast resultfile: %s\n", fileresf);     ij=Tvar[i];
   }     Ndum[ij]++;
   printf("Computing forecasting: result on file '%s' \n", fileresf);   }
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;   ij=1;
    for (i=1; i<= maxncov; i++) {
   if (mobilav==1) {     if((Ndum[i]!=0) && (i<=ncovcol)){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       Tvaraff[ij]=i; /*For printing */
     movingaverage(agedeb, fage, ageminpar, mobaverage);       ij++;
   }     }
    }
   stepsize=(int) (stepm+YEARM-1)/YEARM;   
   if (stepm<=12) stepsize=1;   cptcoveff=ij-1; /*Number of simple covariates*/
    }
   agelim=AGESUP;  
    /*********** Health Expectancies ****************/
   hstepm=1;  
   hstepm=hstepm/stepm;  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;  {
   yp2=modf((yp1*12),&yp);    /* Health expectancies */
   mprojmean=yp;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   yp1=modf((yp2*30.5),&yp);    double age, agelim, hf;
   jprojmean=yp;    double ***p3mat,***varhe;
   if(jprojmean==0) jprojmean=1;    double **dnewm,**doldm;
   if(mprojmean==0) jprojmean=1;    double *xp;
      double **gp, **gm;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    double ***gradg, ***trgradg;
      int theta;
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       k=k+1;    xp=vector(1,npar);
       fprintf(ficresf,"\n#******");    dnewm=matrix(1,nlstate*nlstate,1,npar);
       for(j=1;j<=cptcoveff;j++) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       }    fprintf(ficreseij,"# Health expectancies\n");
       fprintf(ficresf,"******\n");    fprintf(ficreseij,"# Age");
       fprintf(ficresf,"# StartingAge FinalAge");    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      for(j=1; j<=nlstate;j++)
              fprintf(ficreseij," %1d-%1d (SE)",i,j);
          fprintf(ficreseij,"\n");
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  
         fprintf(ficresf,"\n");    if(estepm < stepm){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        printf ("Problem %d lower than %d\n",estepm, stepm);
     }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    else  hstepm=estepm;   
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /* We compute the life expectancy from trapezoids spaced every estepm months
           nhstepm = nhstepm/hstepm;     * This is mainly to measure the difference between two models: for example
               * if stepm=24 months pijx are given only every 2 years and by summing them
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * we are calculating an estimate of the Life Expectancy assuming a linear 
           oldm=oldms;savm=savms;     * progression in between and thus overestimating or underestimating according
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * to the curvature of the survival function. If, for the same date, we 
             * estimate the model with stepm=1 month, we can keep estepm to 24 months
           for (h=0; h<=nhstepm; h++){     * to compare the new estimate of Life expectancy with the same linear 
             if (h==(int) (calagedate+YEARM*cpt)) {     * hypothesis. A more precise result, taking into account a more precise
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);     * curvature will be obtained if estepm is as small as stepm. */
             }  
             for(j=1; j<=nlstate+ndeath;j++) {    /* For example we decided to compute the life expectancy with the smallest unit */
               kk1=0.;kk2=0;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
               for(i=1; i<=nlstate;i++) {                     nhstepm is the number of hstepm from age to agelim 
                 if (mobilav==1)       nstepm is the number of stepm from age to agelin. 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];       Look at hpijx to understand the reason of that which relies in memory size
                 else {       and note for a fixed period like estepm months */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                 }       survival function given by stepm (the optimization length). Unfortunately it
                       means that if the survival funtion is printed only each two years of age and if
               }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               if (h==(int)(calagedate+12*cpt)){       results. So we changed our mind and took the option of the best precision.
                 fprintf(ficresf," %.3f", kk1);    */
                            hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               }  
             }    agelim=AGESUP;
           }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* nhstepm age range expressed in number of stepm */
         }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     }      /* if (stepm >= YEARM) hstepm=1;*/
   }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       gp=matrix(0,nhstepm,1,nlstate*nlstate);
   fclose(ficresf);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
 }  
 /************** Forecasting ******************/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;   
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;      /* Computing Variances of health expectancies */
   char filerespop[FILENAMELENGTH];  
        for(theta=1; theta <=npar; theta++){
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=1; i<=npar; i++){ 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   agelim=AGESUP;        }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        cptj=0;
          for(j=1; j<= nlstate; j++){
            for(i=1; i<=nlstate; i++){
   strcpy(filerespop,"pop");            cptj=cptj+1;
   strcat(filerespop,fileres);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     printf("Problem with forecast resultfile: %s\n", filerespop);            }
   }          }
   printf("Computing forecasting: result on file '%s' \n", filerespop);        }
        
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       
         for(i=1; i<=npar; i++) 
   if (mobilav==1) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     movingaverage(agedeb, fage, ageminpar, mobaverage);        
   }        cptj=0;
         for(j=1; j<= nlstate; j++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(i=1;i<=nlstate;i++){
   if (stepm<=12) stepsize=1;            cptj=cptj+1;
              for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   agelim=AGESUP;  
                gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   hstepm=1;            }
   hstepm=hstepm/stepm;          }
          }
   if (popforecast==1) {        for(j=1; j<= nlstate*nlstate; j++)
     if((ficpop=fopen(popfile,"r"))==NULL) {          for(h=0; h<=nhstepm-1; h++){
       printf("Problem with population file : %s\n",popfile);exit(0);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     }          }
     popage=ivector(0,AGESUP);       } 
     popeffectif=vector(0,AGESUP);     
     popcount=vector(0,AGESUP);  /* End theta */
      
     i=1;         trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
           for(h=0; h<=nhstepm-1; h++)
     imx=i;        for(j=1; j<=nlstate*nlstate;j++)
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
        
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       for(i=1;i<=nlstate*nlstate;i++)
       k=k+1;        for(j=1;j<=nlstate*nlstate;j++)
       fprintf(ficrespop,"\n#******");          varhe[i][j][(int)age] =0.;
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       printf("%d|",(int)age);fflush(stdout);
       }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficrespop,"******\n");       for(h=0;h<=nhstepm-1;h++){
       fprintf(ficrespop,"# Age");        for(k=0;k<=nhstepm-1;k++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       if (popforecast==1)  fprintf(ficrespop," [Population]");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                for(i=1;i<=nlstate*nlstate;i++)
       for (cpt=0; cpt<=0;cpt++) {            for(j=1;j<=nlstate*nlstate;j++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
                }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      /* Computing expectancies */
           nhstepm = nhstepm/hstepm;      for(i=1; i<=nlstate;i++)
                  for(j=1; j<=nlstate;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           oldm=oldms;savm=savms;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              
          /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {          }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }      fprintf(ficreseij,"%3.0f",age );
             for(j=1; j<=nlstate+ndeath;j++) {      cptj=0;
               kk1=0.;kk2=0;      for(i=1; i<=nlstate;i++)
               for(i=1; i<=nlstate;i++) {                      for(j=1; j<=nlstate;j++){
                 if (mobilav==1)          cptj++;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
                 else {        }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      fprintf(ficreseij,"\n");
                 }     
               }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
               if (h==(int)(calagedate+12*cpt)){      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   /*fprintf(ficrespop," %.3f", kk1);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               }    }
             }    printf("\n");
             for(i=1; i<=nlstate;i++){    fprintf(ficlog,"\n");
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){    free_vector(xp,1,npar);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                 }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
             }  }
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  /************ Variance ******************/
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
           }  {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* Variance of health expectancies */
         }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       }    /* double **newm;*/
      double **dnewm,**doldm;
   /******/    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    int k, cptcode;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      double *xp;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    double **gp, **gm;  /* for var eij */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double ***gradg, ***trgradg; /*for var eij */
           nhstepm = nhstepm/hstepm;    double **gradgp, **trgradgp; /* for var p point j */
              double *gpp, *gmp; /* for var p point j */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           oldm=oldms;savm=savms;    double ***p3mat;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double age,agelim, hf;
           for (h=0; h<=nhstepm; h++){    double ***mobaverage;
             if (h==(int) (calagedate+YEARM*cpt)) {    int theta;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    char digit[4];
             }    char digitp[25];
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    char fileresprobmorprev[FILENAMELENGTH];
               for(i=1; i<=nlstate;i++) {                
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        if(popbased==1){
               }      if(mobilav!=0)
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        strcpy(digitp,"-populbased-mobilav-");
             }      else strcpy(digitp,"-populbased-nomobil-");
           }    }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    else 
         }      strcpy(digitp,"-stablbased-");
       }  
    }    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if (popforecast==1) {      }
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);    strcpy(fileresprobmorprev,"prmorprev"); 
   }    sprintf(digit,"%-d",ij);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   fclose(ficrespop);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
 }    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
 /***********************************************/      printf("Problem with resultfile: %s\n", fileresprobmorprev);
 /**************** Main Program *****************/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 /***********************************************/    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 int main(int argc, char *argv[])    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 {    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   double agedeb, agefin,hf;      fprintf(ficresprobmorprev," p.%-d SE",j);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   double fret;    }  
   double **xi,tmp,delta;    fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   double dum; /* Dummy variable */    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   double ***p3mat;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   int *indx;  /*   } */
   char line[MAXLINE], linepar[MAXLINE];    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   char filerest[FILENAMELENGTH];    fprintf(ficresvij,"\n");
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];    xp=vector(1,npar);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    dnewm=matrix(1,nlstate,1,npar);
   int firstobs=1, lastobs=10;    doldm=matrix(1,nlstate,1,nlstate);
   int sdeb, sfin; /* Status at beginning and end */    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   int c,  h , cpt,l;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    gpp=vector(nlstate+1,nlstate+ndeath);
   int mobilav=0,popforecast=0;    gmp=vector(nlstate+1,nlstate+ndeath);
   int hstepm, nhstepm;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    
     if(estepm < stepm){
   double bage, fage, age, agelim, agebase;      printf ("Problem %d lower than %d\n",estepm, stepm);
   double ftolpl=FTOL;    }
   double **prlim;    else  hstepm=estepm;   
   double *severity;    /* For example we decided to compute the life expectancy with the smallest unit */
   double ***param; /* Matrix of parameters */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   double  *p;       nhstepm is the number of hstepm from age to agelim 
   double **matcov; /* Matrix of covariance */       nstepm is the number of stepm from age to agelin. 
   double ***delti3; /* Scale */       Look at hpijx to understand the reason of that which relies in memory size
   double *delti; /* Scale */       and note for a fixed period like k years */
   double ***eij, ***vareij;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double **varpl; /* Variances of prevalence limits by age */       survival function given by stepm (the optimization length). Unfortunately it
   double *epj, vepp;       means that if the survival funtion is printed every two years of age and if
   double kk1, kk2;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;       results. So we changed our mind and took the option of the best precision.
      */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";    agelim = AGESUP;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char z[1]="c", occ;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #include <sys/time.h>      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 #include <time.h>      gp=matrix(0,nhstepm,1,nlstate);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      gm=matrix(0,nhstepm,1,nlstate);
    
   /* long total_usecs;  
   struct timeval start_time, end_time;      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   getcwd(pathcd, size);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   printf("\n%s",version);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");        if (popbased==1) {
     scanf("%s",pathtot);          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
   else{              prlim[i][i]=probs[(int)age][i][ij];
     strcpy(pathtot,argv[1]);          }else{ /* mobilav */ 
   }            for(i=1; i<=nlstate;i++)
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              prlim[i][i]=mobaverage[(int)age][i][ij];
   /*cygwin_split_path(pathtot,path,optionfile);          }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        }
   /* cutv(path,optionfile,pathtot,'\\');*/    
         for(j=1; j<= nlstate; j++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          for(h=0; h<=nhstepm; h++){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   chdir(path);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   replace(pathc,path);          }
         }
 /*-------- arguments in the command line --------*/        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   strcpy(fileres,"r");           as a weighted average of prlim.
   strcat(fileres, optionfilefiname);        */
   strcat(fileres,".txt");    /* Other files have txt extension */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
   /*---------arguments file --------*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        /* end probability of death */
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   strcpy(filereso,"o");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcat(filereso,fileres);   
   if((ficparo=fopen(filereso,"w"))==NULL) {        if (popbased==1) {
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   /* Reads comments: lines beginning with '#' */          }else{ /* mobilav */ 
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);              prlim[i][i]=mobaverage[(int)age][i][ij];
     fgets(line, MAXLINE, ficpar);          }
     puts(line);        }
     fputs(line,ficparo);  
   }        for(j=1; j<= nlstate; j++){
   ungetc(c,ficpar);          for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);          }
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);        }
 while((c=getc(ficpar))=='#' && c!= EOF){        /* This for computing probability of death (h=1 means
     ungetc(c,ficpar);           computed over hstepm matrices product = hstepm*stepm months) 
     fgets(line, MAXLINE, ficpar);           as a weighted average of prlim.
     puts(line);        */
     fputs(line,ficparo);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   ungetc(c,ficpar);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
            /* end probability of death */
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;        for(j=1; j<= nlstate; j++) /* vareij */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   ncovmodel=2+cptcovn;          }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   /* Read guess parameters */          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      } /* End theta */
     fgets(line, MAXLINE, ficpar);  
     puts(line);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     fputs(line,ficparo);  
   }      for(h=0; h<=nhstepm; h++) /* veij */
   ungetc(c,ficpar);        for(j=1; j<=nlstate;j++)
            for(theta=1; theta <=npar; theta++)
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            trgradg[h][j][theta]=gradg[h][theta][j];
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for(theta=1; theta <=npar; theta++)
       fprintf(ficparo,"%1d%1d",i1,j1);          trgradgp[j][theta]=gradgp[theta][j];
       printf("%1d%1d",i,j);    
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         printf(" %lf",param[i][j][k]);      for(i=1;i<=nlstate;i++)
         fprintf(ficparo," %lf",param[i][j][k]);        for(j=1;j<=nlstate;j++)
       }          vareij[i][j][(int)age] =0.;
       fscanf(ficpar,"\n");  
       printf("\n");      for(h=0;h<=nhstepm;h++){
       fprintf(ficparo,"\n");        for(k=0;k<=nhstepm;k++){
     }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
   p=param[1][1];              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);      /* pptj */
     fgets(line, MAXLINE, ficpar);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     puts(line);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     fputs(line,ficparo);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   ungetc(c,ficpar);          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      /*  x centered again */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   for(i=1; i <=nlstate; i++){      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     for(j=1; j <=nlstate+ndeath-1; j++){   
       fscanf(ficpar,"%1d%1d",&i1,&j1);      if (popbased==1) {
       printf("%1d%1d",i,j);        if(mobilav ==0){
       fprintf(ficparo,"%1d%1d",i1,j1);          for(i=1; i<=nlstate;i++)
       for(k=1; k<=ncovmodel;k++){            prlim[i][i]=probs[(int)age][i][ij];
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }else{ /* mobilav */ 
         printf(" %le",delti3[i][j][k]);          for(i=1; i<=nlstate;i++)
         fprintf(ficparo," %le",delti3[i][j][k]);            prlim[i][i]=mobaverage[(int)age][i][ij];
       }        }
       fscanf(ficpar,"\n");      }
       printf("\n");               
       fprintf(ficparo,"\n");      /* This for computing probability of death (h=1 means
     }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   }         as a weighted average of prlim.
   delti=delti3[1][1];      */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /* Reads comments: lines beginning with '#' */        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   while((c=getc(ficpar))=='#' && c!= EOF){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     ungetc(c,ficpar);      }    
     fgets(line, MAXLINE, ficpar);      /* end probability of death */
     puts(line);  
     fputs(line,ficparo);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
   matcov=matrix(1,npar,1,npar);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   for(i=1; i <=npar; i++){        }
     fscanf(ficpar,"%s",&str);      } 
     printf("%s",str);      fprintf(ficresprobmorprev,"\n");
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){      fprintf(ficresvij,"%.0f ",age );
       fscanf(ficpar," %le",&matcov[i][j]);      for(i=1; i<=nlstate;i++)
       printf(" %.5le",matcov[i][j]);        for(j=1; j<=nlstate;j++){
       fprintf(ficparo," %.5le",matcov[i][j]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     }        }
     fscanf(ficpar,"\n");      fprintf(ficresvij,"\n");
     printf("\n");      free_matrix(gp,0,nhstepm,1,nlstate);
     fprintf(ficparo,"\n");      free_matrix(gm,0,nhstepm,1,nlstate);
   }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   for(i=1; i <=npar; i++)      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     for(j=i+1;j<=npar;j++)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       matcov[i][j]=matcov[j][i];    } /* End age */
        free_vector(gpp,nlstate+1,nlstate+ndeath);
   printf("\n");    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     /*-------- Rewriting paramater file ----------*/    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
      strcpy(rfileres,"r");    /* "Rparameterfile */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      strcat(rfileres,".");    /* */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     if((ficres =fopen(rfileres,"w"))==NULL) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficres,"#%s\n",version);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
        fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     /*-------- data file ----------*/    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     if((fic=fopen(datafile,"r"))==NULL)    {    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       printf("Problem with datafile: %s\n", datafile);goto end;  */
     }  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     n= lastobs;  
     severity = vector(1,maxwav);    free_vector(xp,1,npar);
     outcome=imatrix(1,maxwav+1,1,n);    free_matrix(doldm,1,nlstate,1,nlstate);
     num=ivector(1,n);    free_matrix(dnewm,1,nlstate,1,npar);
     moisnais=vector(1,n);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     annais=vector(1,n);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     moisdc=vector(1,n);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     andc=vector(1,n);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agedc=vector(1,n);    fclose(ficresprobmorprev);
     cod=ivector(1,n);    fflush(ficgp);
     weight=vector(1,n);    fflush(fichtm); 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  }  /* end varevsij */
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);  /************ Variance of prevlim ******************/
     s=imatrix(1,maxwav+1,1,n);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     adl=imatrix(1,maxwav+1,1,n);      {
     tab=ivector(1,NCOVMAX);    /* Variance of prevalence limit */
     ncodemax=ivector(1,8);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     i=1;    double **dnewm,**doldm;
     while (fgets(line, MAXLINE, fic) != NULL)    {    int i, j, nhstepm, hstepm;
       if ((i >= firstobs) && (i <=lastobs)) {    int k, cptcode;
            double *xp;
         for (j=maxwav;j>=1;j--){    double *gp, *gm;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double **gradg, **trgradg;
           strcpy(line,stra);    double age,agelim;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int theta;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);     
         }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
            fprintf(ficresvpl,"# Age");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    doldm=matrix(1,nlstate,1,nlstate);
         for (j=ncovcol;j>=1;j--){    
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=1*YEARM; /* Every year of age */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         num[i]=atol(stra);    agelim = AGESUP;
            for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         i=i+1;      gradg=matrix(1,npar,1,nlstate);
       }      gp=vector(1,nlstate);
     }      gm=vector(1,nlstate);
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/      for(theta=1; theta <=npar; theta++){
   imx=i-1; /* Number of individuals */        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /* for (i=1; i<=imx; i++){        }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        for(i=1;i<=nlstate;i++)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          gp[i] = prlim[i][i];
     }*/      
          for(i=1; i<=npar; i++) /* Computes gradient */
   /* for (i=1; i<=imx; i++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      if (s[4][i]==9)  s[4][i]=-1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}        for(i=1;i<=nlstate;i++)
   */          gm[i] = prlim[i][i];
    
   /* Calculation of the number of parameter from char model*/        for(i=1;i<=nlstate;i++)
   Tvar=ivector(1,15);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   Tprod=ivector(1,15);      } /* End theta */
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);      trgradg =matrix(1,nlstate,1,npar);
   Tage=ivector(1,15);        
          for(j=1; j<=nlstate;j++)
   if (strlen(model) >1){        for(theta=1; theta <=npar; theta++)
     j=0, j1=0, k1=1, k2=1;          trgradg[j][theta]=gradg[theta][j];
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');      for(i=1;i<=nlstate;i++)
     cptcovn=j+1;        varpl[i][(int)age] =0.;
     cptcovprod=j1;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     strcpy(modelsav,model);      for(i=1;i<=nlstate;i++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       printf("Error. Non available option model=%s ",model);  
       goto end;      fprintf(ficresvpl,"%.0f ",age );
     }      for(i=1; i<=nlstate;i++)
            fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     for(i=(j+1); i>=1;i--){      fprintf(ficresvpl,"\n");
       cutv(stra,strb,modelsav,'+');      free_vector(gp,1,nlstate);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      free_vector(gm,1,nlstate);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      free_matrix(gradg,1,npar,1,nlstate);
       /*scanf("%d",i);*/      free_matrix(trgradg,1,nlstate,1,npar);
       if (strchr(strb,'*')) {    } /* End age */
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {    free_vector(xp,1,npar);
           cptcovprod--;    free_matrix(doldm,1,nlstate,1,npar);
           cutv(strb,stre,strd,'V');    free_matrix(dnewm,1,nlstate,1,nlstate);
           Tvar[i]=atoi(stre);  
           cptcovage++;  }
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/  /************ Variance of one-step probabilities  ******************/
         }  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
         else if (strcmp(strd,"age")==0) {  {
           cptcovprod--;    int i, j=0,  i1, k1, l1, t, tj;
           cutv(strb,stre,strc,'V');    int k2, l2, j1,  z1;
           Tvar[i]=atoi(stre);    int k=0,l, cptcode;
           cptcovage++;    int first=1, first1;
           Tage[cptcovage]=i;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         }    double **dnewm,**doldm;
         else {    double *xp;
           cutv(strb,stre,strc,'V');    double *gp, *gm;
           Tvar[i]=ncovcol+k1;    double **gradg, **trgradg;
           cutv(strb,strc,strd,'V');    double **mu;
           Tprod[k1]=i;    double age,agelim, cov[NCOVMAX];
           Tvard[k1][1]=atoi(strc);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           Tvard[k1][2]=atoi(stre);    int theta;
           Tvar[cptcovn+k2]=Tvard[k1][1];    char fileresprob[FILENAMELENGTH];
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    char fileresprobcov[FILENAMELENGTH];
           for (k=1; k<=lastobs;k++)    char fileresprobcor[FILENAMELENGTH];
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;    double ***varpij;
           k2=k2+2;  
         }    strcpy(fileresprob,"prob"); 
       }    strcat(fileresprob,fileres);
       else {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      printf("Problem with resultfile: %s\n", fileresprob);
        /*  scanf("%d",i);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       cutv(strd,strc,strb,'V');    }
       Tvar[i]=atoi(strc);    strcpy(fileresprobcov,"probcov"); 
       }    strcat(fileresprobcov,fileres);
       strcpy(modelsav,stra);      if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      printf("Problem with resultfile: %s\n", fileresprobcov);
         scanf("%d",i);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }    }
 }    strcpy(fileresprobcor,"probcor"); 
      strcat(fileresprobcor,fileres);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   printf("cptcovprod=%d ", cptcovprod);      printf("Problem with resultfile: %s\n", fileresprobcor);
   scanf("%d ",i);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     fclose(fic);    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     /*  if(mle==1){*/    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     if (weightopt != 1) { /* Maximisation without weights*/    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     }    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     agev=matrix(1,maxwav,1,imx);    
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     for (i=1; i<=imx; i++) {    fprintf(ficresprob,"# Age");
       for(m=2; (m<= maxwav); m++) {    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    fprintf(ficresprobcov,"# Age");
          anint[m][i]=9999;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
          s[m][i]=-1;    fprintf(ficresprobcov,"# Age");
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     for (i=1; i<=imx; i++)  {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       for(m=1; (m<= maxwav); m++){      }  
         if(s[m][i] >0){   /* fprintf(ficresprob,"\n");
           if (s[m][i] >= nlstate+1) {    fprintf(ficresprobcov,"\n");
             if(agedc[i]>0)    fprintf(ficresprobcor,"\n");
               if(moisdc[i]!=99 && andc[i]!=9999)   */
                 agev[m][i]=agedc[i];   xp=vector(1,npar);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
            else {    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
               if (andc[i]!=9999){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
               agev[m][i]=-1;    first=1;
               }    fprintf(ficgp,"\n# Routine varprob");
             }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           }    fprintf(fichtm,"\n");
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
             if(mint[m][i]==99 || anint[m][i]==9999)    fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
               agev[m][i]=1;    file %s<br>\n",optionfilehtmcov);
             else if(agev[m][i] <agemin){    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
               agemin=agev[m][i];  and drawn. It helps understanding how is the covariance between two incidences.\
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
             }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
             else if(agev[m][i] >agemax){  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
               agemax=agev[m][i];  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  standard deviations wide on each axis. <br>\
             }   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
             /*agev[m][i]=anint[m][i]-annais[i];*/   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
             /*   agev[m][i] = age[i]+2*m;*/  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
           }  
           else { /* =9 */    cov[1]=1;
             agev[m][i]=1;    tj=cptcoveff;
             s[m][i]=-1;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           }    j1=0;
         }    for(t=1; t<=tj;t++){
         else /*= 0 Unknown */      for(i1=1; i1<=ncodemax[t];i1++){ 
           agev[m][i]=1;        j1++;
       }        if  (cptcovn>0) {
              fprintf(ficresprob, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (i=1; i<=imx; i++)  {          fprintf(ficresprob, "**********\n#\n");
       for(m=1; (m<= maxwav); m++){          fprintf(ficresprobcov, "\n#********** Variable "); 
         if (s[m][i] > (nlstate+ndeath)) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           printf("Error: Wrong value in nlstate or ndeath\n");            fprintf(ficresprobcov, "**********\n#\n");
           goto end;          
         }          fprintf(ficgp, "\n#********** Variable "); 
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficgp, "**********\n#\n");
           
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          
           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     free_vector(severity,1,maxwav);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_imatrix(outcome,1,maxwav+1,1,n);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     free_vector(moisnais,1,n);          
     free_vector(annais,1,n);          fprintf(ficresprobcor, "\n#********** Variable ");    
     /* free_matrix(mint,1,maxwav,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        free_matrix(anint,1,maxwav,1,n);*/          fprintf(ficresprobcor, "**********\n#");    
     free_vector(moisdc,1,n);        }
     free_vector(andc,1,n);        
         for (age=bage; age<=fage; age ++){ 
              cov[2]=age;
     wav=ivector(1,imx);          for (k=1; k<=cptcovn;k++) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          }
              for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     /* Concatenates waves */          for (k=1; k<=cptcovprod;k++)
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       Tcode=ivector(1,100);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          gp=vector(1,(nlstate)*(nlstate+ndeath));
       ncodemax[1]=1;          gm=vector(1,(nlstate)*(nlstate+ndeath));
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      
                for(theta=1; theta <=npar; theta++){
    codtab=imatrix(1,100,1,10);            for(i=1; i<=npar; i++)
    h=0;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
    m=pow(2,cptcoveff);            
              pmij(pmmij,cov,ncovmodel,xp,nlstate);
    for(k=1;k<=cptcoveff; k++){            
      for(i=1; i <=(m/pow(2,k));i++){            k=0;
        for(j=1; j <= ncodemax[k]; j++){            for(i=1; i<= (nlstate); i++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              for(j=1; j<=(nlstate+ndeath);j++){
            h++;                k=k+1;
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                gp[k]=pmmij[i][j];
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/              }
          }            }
        }            
      }            for(i=1; i<=npar; i++)
    }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      
       codtab[1][2]=1;codtab[2][2]=2; */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
    /* for(i=1; i <=m ;i++){            k=0;
       for(k=1; k <=cptcovn; k++){            for(i=1; i<=(nlstate); i++){
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);              for(j=1; j<=(nlstate+ndeath);j++){
       }                k=k+1;
       printf("\n");                gm[k]=pmmij[i][j];
       }              }
       scanf("%d",i);*/            }
           
    /* Calculates basic frequencies. Computes observed prevalence at single age            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
        and prints on file fileres'p'. */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
      
              for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(theta=1; theta <=npar; theta++)
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              trgradg[j][theta]=gradg[theta][j];
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     /* For Powell, parameters are in a vector p[] starting at p[1]          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
     if(mle==1){          pmij(pmmij,cov,ncovmodel,x,nlstate);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          
     }          k=0;
              for(i=1; i<=(nlstate); i++){
     /*--------- results files --------------*/            for(j=1; j<=(nlstate+ndeath);j++){
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);              k=k+1;
                mu[k][(int) age]=pmmij[i][j];
             }
    jk=1;          }
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
    for(i=1,jk=1; i <=nlstate; i++){              varpij[i][j][(int)age] = doldm[i][j];
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)          /*printf("\n%d ",(int)age);
          {            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            printf("%d%d ",i,k);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
            fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
            for(j=1; j <=ncovmodel; j++){            }*/
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);          fprintf(ficresprob,"\n%d ",(int)age);
              jk++;          fprintf(ficresprobcov,"\n%d ",(int)age);
            }          fprintf(ficresprobcor,"\n%d ",(int)age);
            printf("\n");  
            fprintf(ficres,"\n");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
          }            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
      }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
    }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
  if(mle==1){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     /* Computing hessian and covariance matrix */          }
     ftolhess=ftol; /* Usually correct */          i=0;
     hesscov(matcov, p, npar, delti, ftolhess, func);          for (k=1; k<=(nlstate);k++){
  }            for (l=1; l<=(nlstate+ndeath);l++){ 
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");              i=i++;
     printf("# Scales (for hessian or gradient estimation)\n");              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
      for(i=1,jk=1; i <=nlstate; i++){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       for(j=1; j <=nlstate+ndeath; j++){              for (j=1; j<=i;j++){
         if (j!=i) {                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
           fprintf(ficres,"%1d%1d",i,j);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
           printf("%1d%1d",i,j);              }
           for(k=1; k<=ncovmodel;k++){            }
             printf(" %.5e",delti[jk]);          }/* end of loop for state */
             fprintf(ficres," %.5e",delti[jk]);        } /* end of loop for age */
             jk++;  
           }        /* Confidence intervalle of pij  */
           printf("\n");        /*
           fprintf(ficres,"\n");          fprintf(ficgp,"\nset noparametric;unset label");
         }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       }          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
      }          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
              fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     k=1;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        */
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       i1=(i-1)/(ncovmodel*nlstate)+1;        first1=1;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        for (k2=1; k2<=(nlstate);k2++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       fprintf(ficres,"%3d",i);            if(l2==k2) continue;
       printf("%3d",i);            j=(k2-1)*(nlstate+ndeath)+l2;
       for(j=1; j<=i;j++){            for (k1=1; k1<=(nlstate);k1++){
         fprintf(ficres," %.5e",matcov[i][j]);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         printf(" %.5e",matcov[i][j]);                if(l1==k1) continue;
       }                i=(k1-1)*(nlstate+ndeath)+l1;
       fprintf(ficres,"\n");                if(i<=j) continue;
       printf("\n");                for (age=bage; age<=fage; age ++){ 
       k++;                  if ((int)age %5==0){
     }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                        v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     while((c=getc(ficpar))=='#' && c!= EOF){                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       ungetc(c,ficpar);                    mu1=mu[i][(int) age]/stepm*YEARM ;
       fgets(line, MAXLINE, ficpar);                    mu2=mu[j][(int) age]/stepm*YEARM;
       puts(line);                    c12=cv12/sqrt(v1*v2);
       fputs(line,ficparo);                    /* Computing eigen value of matrix of covariance */
     }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     ungetc(c,ficpar);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     estepm=0;                    /* Eigen vectors */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     if (estepm==0 || estepm < stepm) estepm=stepm;                    /*v21=sqrt(1.-v11*v11); *//* error */
     if (fage <= 2) {                    v21=(lc1-v1)/cv12*v11;
       bage = ageminpar;                    v12=-v21;
       fage = agemaxpar;                    v22=v11;
     }                    tnalp=v21/v11;
                        if(first1==1){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                      first1=0;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    }
                      fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     while((c=getc(ficpar))=='#' && c!= EOF){                    /*printf(fignu*/
     ungetc(c,ficpar);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     fgets(line, MAXLINE, ficpar);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     puts(line);                    if(first==1){
     fputs(line,ficparo);                      first=0;
   }                      fprintf(ficgp,"\nset parametric;unset label");
   ungetc(c,ficpar);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   while((c=getc(ficpar))=='#' && c!= EOF){                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     ungetc(c,ficpar);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     fgets(line, MAXLINE, ficpar);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     puts(line);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     fputs(line,ficparo);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   ungetc(c,ficpar);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                    }else{
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                      first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   fscanf(ficpar,"pop_based=%d\n",&popbased);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   fprintf(ficparo,"pop_based=%d\n",popbased);                        fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   fprintf(ficres,"pop_based=%d\n",popbased);                        fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   while((c=getc(ficpar))=='#' && c!= EOF){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     ungetc(c,ficpar);                    }/* if first */
     fgets(line, MAXLINE, ficpar);                  } /* age mod 5 */
     puts(line);                } /* end loop age */
     fputs(line,ficparo);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   }                first=1;
   ungetc(c,ficpar);              } /*l12 */
             } /* k12 */
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          } /*l1 */
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        }/* k1 */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
 while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     ungetc(c,ficpar);    free_vector(xp,1,npar);
     fgets(line, MAXLINE, ficpar);    fclose(ficresprob);
     puts(line);    fclose(ficresprobcov);
     fputs(line,ficparo);    fclose(ficresprobcor);
   }    fflush(ficgp);
   ungetc(c,ficpar);    fflush(fichtmcov);
   }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
 /*------------ gnuplot -------------*/                    int popforecast, int estepm ,\
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);                    double jprev1, double mprev1,double anprev1, \
                      double jprev2, double mprev2,double anprev2){
 /*------------ free_vector  -------------*/    int jj1, k1, i1, cpt;
  chdir(path);    /*char optionfilehtm[FILENAMELENGTH];*/
    /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
  free_ivector(wav,1,imx);  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    /*   } */
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
  fclose(ficparo);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
  fclose(ficres);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
    - Life expectancies by age and initial health status (estepm=%2d months): \
 /*--------- index.htm --------*/     <a href=\"%s\">%s</a> <br>\n</li>", \
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
               estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   /*--------------- Prevalence limit --------------*/  
    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);   m=cptcoveff;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }   jj1=0;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);   for(k1=1; k1<=m;k1++){
   fprintf(ficrespl,"#Prevalence limit\n");     for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficrespl,"#Age ");       jj1++;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);       if (cptcovn > 0) {
   fprintf(ficrespl,"\n");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for (cpt=1; cpt<=cptcoveff;cpt++) 
   prlim=matrix(1,nlstate,1,nlstate);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       /* Pij */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   k=0;       /* Quasi-incidences */
   agebase=ageminpar;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   agelim=agemaxpar;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   ftolpl=1.e-10;  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   i1=cptcoveff;         /* Stable prevalence in each health state */
   if (cptcovn < 1){i1=1;}         for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   for(cptcov=1;cptcov<=i1;cptcov++){  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         }
         k=k+1;       for(cpt=1; cpt<=nlstate;cpt++) {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         fprintf(ficrespl,"\n#******");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
         for(j=1;j<=cptcoveff;j++)       }
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
         fprintf(ficrespl,"******\n");  health expectancies in states (1) and (2): %s%d.png<br>\
          <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
         for (age=agebase; age<=agelim; age++){     } /* end i1 */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   }/* End k1 */
           fprintf(ficrespl,"%.0f",age );   fprintf(fichtm,"</ul>");
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
         }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
       }   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     }   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
   fclose(ficrespl);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
   /*------------- h Pij x at various ages ------------*/   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
     - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);           rfileres,rfileres,\
   if((ficrespij=fopen(filerespij,"w"))==NULL) {           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
   }           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
   printf("Computing pij: result on file '%s' \n", filerespij);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
             subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
   stepsize=(int) (stepm+YEARM-1)/YEARM;           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   /*if (stepm<=24) stepsize=2;*/  
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   agelim=AGESUP;  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   hstepm=stepsize*YEARM; /* Every year of age */  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  /*      <br>",fileres,fileres,fileres,fileres); */
    /*  else  */
   k=0;  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   for(cptcov=1;cptcov<=i1;cptcov++){  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;   m=cptcoveff;
         fprintf(ficrespij,"\n#****** ");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   jj1=0;
         fprintf(ficrespij,"******\n");   for(k1=1; k1<=m;k1++){
             for(i1=1; i1<=ncodemax[k1];i1++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       jj1++;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       if (cptcovn > 0) {
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         for (cpt=1; cpt<=cptcoveff;cpt++) 
           oldm=oldms;savm=savms;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           fprintf(ficrespij,"# Age");       }
           for(i=1; i<=nlstate;i++)       for(cpt=1; cpt<=nlstate;cpt++) {
             for(j=1; j<=nlstate+ndeath;j++)         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
               fprintf(ficrespij," %1d-%1d",i,j);  interval) in state (%d): %s%d%d.png <br>\
           fprintf(ficrespij,"\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
           for (h=0; h<=nhstepm; h++){       }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );     } /* end i1 */
             for(i=1; i<=nlstate;i++)   }/* End k1 */
               for(j=1; j<=nlstate+ndeath;j++)   fprintf(fichtm,"</ul>");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   fflush(fichtm);
             fprintf(ficrespij,"\n");  }
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /******************* Gnuplot file **************/
           fprintf(ficrespij,"\n");  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         }  
     }    char dirfileres[132],optfileres[132];
   }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   fclose(ficrespij);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
   /*---------- Forecasting ------------------*/    /*#ifdef windows */
   if((stepm == 1) && (strcmp(model,".")==0)){    fprintf(ficgp,"cd \"%s\" \n",pathc);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      /*#endif */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    m=pow(2,cptcoveff);
     free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    strcpy(dirfileres,optionfilefiname);
     free_vector(weight,1,n);}    strcpy(optfileres,"vpl");
   else{   /* 1eme*/
     erreur=108;    for (cpt=1; cpt<= nlstate ; cpt ++) {
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);     for (k1=1; k1<= m ; k1 ++) {
   }       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
         fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   /*---------- Health expectancies and variances ------------*/  set ylabel \"Probability\" \n\
   set ter png small\n\
   strcpy(filerest,"t");  set size 0.65,0.65\n\
   strcat(filerest,fileres);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;       for (i=1; i<= nlstate ; i ++) {
   }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
   strcpy(filerese,"e");       for (i=1; i<= nlstate ; i ++) {
   strcat(filerese,fileres);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   if((ficreseij=fopen(filerese,"w"))==NULL) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);       } 
   }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
  strcpy(fileresv,"v");         else fprintf(ficgp," \%%*lf (\%%*lf)");
   strcat(fileresv,fileres);       }  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);     }
   }    }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    /*2 eme*/
     
   k=0;    for (k1=1; k1<= m ; k1 ++) { 
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       k=k+1;      
       fprintf(ficrest,"\n#****** ");      for (i=1; i<= nlstate+1 ; i ++) {
       for(j=1;j<=cptcoveff;j++)        k=2*i;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       fprintf(ficrest,"******\n");        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficreseij,"\n#****** ");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(j=1;j<=cptcoveff;j++)        }   
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       fprintf(ficreseij,"******\n");        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       fprintf(ficresvij,"\n#****** ");        for (j=1; j<= nlstate+1 ; j ++) {
       for(j=1;j<=cptcoveff;j++)          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficresvij,"******\n");        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       oldm=oldms;savm=savms;        for (j=1; j<= nlstate+1 ; j ++) {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       oldm=oldms;savm=savms;        }   
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
            else fprintf(ficgp,"\" t\"\" w l 0,");
       }
      }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    /*3eme*/
       fprintf(ficrest,"\n");    
     for (k1=1; k1<= m ; k1 ++) { 
       epj=vector(1,nlstate+1);      for (cpt=1; cpt<= nlstate ; cpt ++) {
       for(age=bage; age <=fage ;age++){        k=2+nlstate*(2*cpt-2);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         if (popbased==1) {        fprintf(ficgp,"set ter png small\n\
           for(i=1; i<=nlstate;i++)  set size 0.65,0.65\n\
             prlim[i][i]=probs[(int)age][i][k];  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficrest," %4.0f",age);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           }          
           epj[nlstate+1] +=epj[j];        */
         }        for (i=1; i< nlstate ; i ++) {
         for(i=1, vepp=0.;i <=nlstate;i++)          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           for(j=1;j <=nlstate;j++)          
             vepp += vareij[i][j][(int)age];        } 
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));      }
         for(j=1;j <=nlstate;j++){    }
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));    
         }    /* CV preval stable (period) */
         fprintf(ficrest,"\n");    for (k1=1; k1<= m ; k1 ++) { 
       }      for (cpt=1; cpt<=nlstate ; cpt ++) {
     }        k=3;
   }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   fclose(ficreseij);  set ter png small\nset size 0.65,0.65\n\
   fclose(ficresvij);  unset log y\n\
   fclose(ficrest);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   fclose(ficpar);        
   free_vector(epj,1,nlstate+1);        for (i=1; i< nlstate ; i ++)
            fprintf(ficgp,"+$%d",k+i+1);
   /*------- Variance limit prevalence------*/          fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
   strcpy(fileresvpl,"vpl");        l=3+(nlstate+ndeath)*cpt;
   strcat(fileresvpl,fileres);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        for (i=1; i< nlstate ; i ++) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          l=3+(nlstate+ndeath)*cpt;
     exit(0);          fprintf(ficgp,"+$%d",l+i+1);
   }        }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
   k=0;    }  
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* proba elementaires */
       k=k+1;    for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficresvpl,"\n#****** ");      for(k=1; k <=(nlstate+ndeath); k++){
       for(j=1;j<=cptcoveff;j++)        if (k != i) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(j=1; j <=ncovmodel; j++){
       fprintf(ficresvpl,"******\n");            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
                  jk++; 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            fprintf(ficgp,"\n");
       oldm=oldms;savm=savms;          }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        }
     }      }
  }     }
   
   fclose(ficresvpl);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
   /*---------- End : free ----------------*/         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);         if (ng==2)
             fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         else
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);           fprintf(ficgp,"\nset title \"Probability\"\n");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           i=1;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);         for(k2=1; k2<=nlstate; k2++) {
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);           k3=i;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);           for(k=1; k<=(nlstate+ndeath); k++) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);             if (k != k2){
                 if(ng==2)
   free_matrix(matcov,1,npar,1,npar);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   free_vector(delti,1,npar);               else
   free_matrix(agev,1,maxwav,1,imx);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);               ij=1;
                for(j=3; j <=ncovmodel; j++) {
   if(erreur >0)                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     printf("End of Imach with error or warning %d\n",erreur);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   else   printf("End of Imach\n");                   ij++;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                 }
                   else
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   /*printf("Total time was %d uSec.\n", total_usecs);*/               }
   /*------ End -----------*/               fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
  end:                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
 #ifdef windows                 ij=1;
   /* chdir(pathcd);*/                 for(j=3; j <=ncovmodel; j++){
 #endif                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
  /*system("wgnuplot graph.plt");*/                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
  /*system("../gp37mgw/wgnuplot graph.plt");*/                     ij++;
  /*system("cd ../gp37mgw");*/                   }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                   else
  strcpy(plotcmd,GNUPLOTPROGRAM);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  strcat(plotcmd," ");                 }
  strcat(plotcmd,optionfilegnuplot);                 fprintf(ficgp,")");
  system(plotcmd);               }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 #ifdef windows               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   while (z[0] != 'q') {               i=i+ncovmodel;
     /* chdir(path); */             }
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");           } /* end k */
     scanf("%s",z);         } /* end k2 */
     if (z[0] == 'c') system("./imach");       } /* end jk */
     else if (z[0] == 'e') system(optionfilehtm);     } /* end ng */
     else if (z[0] == 'g') system(plotcmd);     fflush(ficgp); 
     else if (z[0] == 'q') exit(0);  }  /* end gnuplot */
   }  
 #endif  
 }  /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Localtime (at start):%s",strstart);
     fprintf(ficlog,"Localtime (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

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  Added in v.1.91


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